Uberon editors
This is an ontology that collects all of the core uberon, plus ALL
gross anatomical ontologies for metazoans.
Uberon importer for metazoan structures
Uberon ontologies with the prefix 'collected' are ontologies that
import the core Uberon ontology together with one or more external
typically species-centric ontologies plus *bridging* axioms that
connect Uberon to the species-centric ontology. Bridging axioms may be
direct equivalence axioms, taxonomic equivalence axioms, or subclass
axioms. See the Uberon homepage for details.
Includes Ontology(OntologyID(Anonymous-18)) [Axioms: 1 Logical Axioms: 0]Includes Ontology(OntologyID(Anonymous-39)) [Axioms: 778 Logical Axioms: 307]Includes Ontology(OntologyID(OntologyIRI(<http://purl.obolibrary.org/obo/ceph.owl>) VersionIRI(<http://purl.obolibrary.org/obo/ceph/releases/2015-03-15/ceph.owl>))) [Axioms: 4508 Logical Axioms: 1463]Includes Ontology(OntologyID(OntologyIRI(<http://purl.obolibrary.org/obo/cteno.owl>) VersionIRI(<null>))) [Axioms: 349 Logical Axioms: 125]Includes Ontology(OntologyID(OntologyIRI(<http://purl.obolibrary.org/obo/dhba.owl>) VersionIRI(<null>))) [Axioms: 39823 Logical Axioms: 6633]Includes Ontology(OntologyID(OntologyIRI(<http://purl.obolibrary.org/obo/dmba.owl>) VersionIRI(<null>))) [Axioms: 32323 Logical Axioms: 5383]Includes Ontology(OntologyID(OntologyIRI(<http://purl.obolibrary.org/obo/ehdaa2.owl>) VersionIRI(<null>))) [Axioms: 17898 Logical Axioms: 12108]Includes Ontology(OntologyID(OntologyIRI(<http://purl.obolibrary.org/obo/fbbt.owl>) VersionIRI(<http://purl.obolibrary.org/obo/fbbt/2015-03-11/fbbt.owl>))) [Axioms: 64250 Logical Axioms: 28913]Includes Ontology(OntologyID(OntologyIRI(<http://purl.obolibrary.org/obo/fbdv.owl>) VersionIRI(<http://purl.obolibrary.org/obo/fbdv/2015-07-02/fbdv.owl>))) [Axioms: 2262 Logical Axioms: 660]Includes Ontology(OntologyID(OntologyIRI(<http://purl.obolibrary.org/obo/hba.owl>) VersionIRI(<null>))) [Axioms: 19156 Logical Axioms: 3677]Includes Ontology(OntologyID(OntologyIRI(<http://purl.obolibrary.org/obo/ma.owl>) VersionIRI(<http://purl.obolibrary.org/obo/ma/releases/2014-07-14/ma.owl>))) [Axioms: 11088 Logical Axioms: 4103]Includes Ontology(OntologyID(OntologyIRI(<http://purl.obolibrary.org/obo/mba.owl>) VersionIRI(<null>))) [Axioms: 14827 Logical Axioms: 2467]Includes Ontology(OntologyID(OntologyIRI(<http://purl.obolibrary.org/obo/pba.owl>) VersionIRI(<null>))) [Axioms: 3127 Logical Axioms: 517]Includes Ontology(OntologyID(OntologyIRI(<http://purl.obolibrary.org/obo/poro.owl>) VersionIRI(<http://purl.obolibrary.org/obo/poro/releases/2015-03-15/poro.owl>))) [Axioms: 3418 Logical Axioms: 1044]Includes Ontology(OntologyID(OntologyIRI(<http://purl.obolibrary.org/obo/uberon/bridge/cl-bridge-to-ehdaa2.owl>) VersionIRI(<http://purl.obolibrary.org/obo/uberon/bridge/cl-bridge-to-ehdaa2/2014-05-27/uberon/bridge/cl-bridge-to-ehdaa2.owl>))) [Axioms: 157 Logical Axioms: 11]Includes Ontology(OntologyID(OntologyIRI(<http://purl.obolibrary.org/obo/uberon/bridge/cl-bridge-to-emapa.owl>) VersionIRI(<http://purl.obolibrary.org/obo/uberon/bridge/cl-bridge-to-emapa/2014-05-27/uberon/bridge/cl-bridge-to-emapa.owl>))) [Axioms: 166 Logical Axioms: 13]Includes Ontology(OntologyID(OntologyIRI(<http://purl.obolibrary.org/obo/uberon/bridge/cl-bridge-to-fbbt.owl>) VersionIRI(<http://purl.obolibrary.org/obo/uberon/bridge/cl-bridge-to-fbbt/2014-05-27/uberon/bridge/cl-bridge-to-fbbt.owl>))) [Axioms: 412 Logical Axioms: 62]Includes Ontology(OntologyID(OntologyIRI(<http://purl.obolibrary.org/obo/uberon/bridge/cl-bridge-to-fma.owl>) VersionIRI(<http://purl.obolibrary.org/obo/uberon/bridge/cl-bridge-to-fma/2014-05-27/uberon/bridge/cl-bridge-to-fma.owl>))) [Axioms: 3608 Logical Axioms: 700]Includes Ontology(OntologyID(OntologyIRI(<http://purl.obolibrary.org/obo/uberon/bridge/cl-bridge-to-ma.owl>) VersionIRI(<http://purl.obolibrary.org/obo/uberon/bridge/cl-bridge-to-ma/2014-05-27/uberon/bridge/cl-bridge-to-ma.owl>))) [Axioms: 144 Logical Axioms: 8]Includes Ontology(OntologyID(OntologyIRI(<http://purl.obolibrary.org/obo/uberon/bridge/cl-bridge-to-wbbt.owl>) VersionIRI(<http://purl.obolibrary.org/obo/uberon/bridge/cl-bridge-to-wbbt/2014-05-27/uberon/bridge/cl-bridge-to-wbbt.owl>))) [Axioms: 252 Logical Axioms: 30]Includes Ontology(OntologyID(OntologyIRI(<http://purl.obolibrary.org/obo/uberon/bridge/cl-bridge-to-xao.owl>) VersionIRI(<http://purl.obolibrary.org/obo/uberon/bridge/cl-bridge-to-xao/2014-05-27/uberon/bridge/cl-bridge-to-xao.owl>))) [Axioms: 147 Logical Axioms: 9]Includes Ontology(OntologyID(OntologyIRI(<http://purl.obolibrary.org/obo/uberon/bridge/cl-bridge-to-zfa.owl>) VersionIRI(<http://purl.obolibrary.org/obo/uberon/bridge/cl-bridge-to-zfa/2014-05-27/uberon/bridge/cl-bridge-to-zfa.owl>))) [Axioms: 2182 Logical Axioms: 416]Includes Ontology(OntologyID(OntologyIRI(<http://purl.obolibrary.org/obo/uberon/bridge/collected-adult-mammal.owl>) VersionIRI(<null>))) [Axioms: 0 Logical Axioms: 0]Includes Ontology(OntologyID(OntologyIRI(<http://purl.obolibrary.org/obo/uberon/bridge/collected-amniote.owl>) VersionIRI(<null>))) [Axioms: 0 Logical Axioms: 0]Includes Ontology(OntologyID(OntologyIRI(<http://purl.obolibrary.org/obo/uberon/bridge/collected-embryonic-mammal.owl>) VersionIRI(<null>))) [Axioms: 0 Logical Axioms: 0]Includes Ontology(OntologyID(OntologyIRI(<http://purl.obolibrary.org/obo/uberon/bridge/collected-mammal.owl>) VersionIRI(<null>))) [Axioms: 0 Logical Axioms: 0]Includes Ontology(OntologyID(OntologyIRI(<http://purl.obolibrary.org/obo/uberon/bridge/collected-teleost.owl>) VersionIRI(<null>))) [Axioms: 0 Logical Axioms: 0]Includes Ontology(OntologyID(OntologyIRI(<http://purl.obolibrary.org/obo/uberon/bridge/collected-tetrapod.owl>) VersionIRI(<null>))) [Axioms: 0 Logical Axioms: 0]Includes Ontology(OntologyID(OntologyIRI(<http://purl.obolibrary.org/obo/uberon/bridge/collected-vertebrate.owl>) VersionIRI(<null>))) [Axioms: 0 Logical Axioms: 0]Includes Ontology(OntologyID(OntologyIRI(<http://purl.obolibrary.org/obo/uberon/bridge/uberon-bridge-to-dhba.owl>) VersionIRI(<http://purl.obolibrary.org/obo/uberon/bridge/uberon-bridge-to-dhba/2018-11-25/uberon/bridge/uberon-bridge-to-dhba.owl>))) [Axioms: 3900 Logical Axioms: 762]Includes Ontology(OntologyID(OntologyIRI(<http://purl.obolibrary.org/obo/uberon/bridge/uberon-bridge-to-dmba.owl>) VersionIRI(<http://purl.obolibrary.org/obo/uberon/bridge/uberon-bridge-to-dmba/2018-11-25/uberon/bridge/uberon-bridge-to-dmba.owl>))) [Axioms: 1412 Logical Axioms: 262]Includes Ontology(OntologyID(OntologyIRI(<http://purl.obolibrary.org/obo/uberon/bridge/uberon-bridge-to-ehdaa2.owl>) VersionIRI(<http://purl.obolibrary.org/obo/uberon/bridge/uberon-bridge-to-ehdaa2/2018-11-25/uberon/bridge/uberon-bridge-to-ehdaa2.owl>))) [Axioms: 7471 Logical Axioms: 1471]Includes Ontology(OntologyID(OntologyIRI(<http://purl.obolibrary.org/obo/uberon/bridge/uberon-bridge-to-emapa.owl>) VersionIRI(<http://purl.obolibrary.org/obo/uberon/bridge/uberon-bridge-to-emapa/2018-11-25/uberon/bridge/uberon-bridge-to-emapa.owl>))) [Axioms: 22009 Logical Axioms: 4371]Includes Ontology(OntologyID(OntologyIRI(<http://purl.obolibrary.org/obo/uberon/bridge/uberon-bridge-to-fbbt.owl>) VersionIRI(<http://purl.obolibrary.org/obo/uberon/bridge/uberon-bridge-to-fbbt/2018-11-25/uberon/bridge/uberon-bridge-to-fbbt.owl>))) [Axioms: 1242 Logical Axioms: 227]Includes Ontology(OntologyID(OntologyIRI(<http://purl.obolibrary.org/obo/uberon/bridge/uberon-bridge-to-fbdv.owl>) VersionIRI(<http://purl.obolibrary.org/obo/uberon/bridge/uberon-bridge-to-fbdv/2018-11-25/uberon/bridge/uberon-bridge-to-fbdv.owl>))) [Axioms: 179 Logical Axioms: 15]Includes Ontology(OntologyID(OntologyIRI(<http://purl.obolibrary.org/obo/uberon/bridge/uberon-bridge-to-hba.owl>) VersionIRI(<http://purl.obolibrary.org/obo/uberon/bridge/uberon-bridge-to-hba/2018-11-25/uberon/bridge/uberon-bridge-to-hba.owl>))) [Axioms: 2978 Logical Axioms: 575]Includes Ontology(OntologyID(OntologyIRI(<http://purl.obolibrary.org/obo/uberon/bridge/uberon-bridge-to-ma.owl>) VersionIRI(<http://purl.obolibrary.org/obo/uberon/bridge/uberon-bridge-to-ma/2018-11-25/uberon/bridge/uberon-bridge-to-ma.owl>))) [Axioms: 15474 Logical Axioms: 3076]Includes Ontology(OntologyID(OntologyIRI(<http://purl.obolibrary.org/obo/uberon/bridge/uberon-bridge-to-mba.owl>) VersionIRI(<http://purl.obolibrary.org/obo/uberon/bridge/uberon-bridge-to-mba/2018-11-25/uberon/bridge/uberon-bridge-to-mba.owl>))) [Axioms: 2779 Logical Axioms: 535]Includes Ontology(OntologyID(OntologyIRI(<http://purl.obolibrary.org/obo/uberon/bridge/uberon-bridge-to-pba.owl>) VersionIRI(<http://purl.obolibrary.org/obo/uberon/bridge/uberon-bridge-to-pba/2018-11-25/uberon/bridge/uberon-bridge-to-pba.owl>))) [Axioms: 597 Logical Axioms: 99]Includes Ontology(OntologyID(OntologyIRI(<http://purl.obolibrary.org/obo/uberon/bridge/uberon-bridge-to-wbbt.owl>) VersionIRI(<http://purl.obolibrary.org/obo/uberon/bridge/uberon-bridge-to-wbbt/2018-11-25/uberon/bridge/uberon-bridge-to-wbbt.owl>))) [Axioms: 495 Logical Axioms: 79]Includes Ontology(OntologyID(OntologyIRI(<http://purl.obolibrary.org/obo/uberon/bridge/uberon-bridge-to-wbls.owl>) VersionIRI(<http://purl.obolibrary.org/obo/uberon/bridge/uberon-bridge-to-wbls/2018-11-25/uberon/bridge/uberon-bridge-to-wbls.owl>))) [Axioms: 178 Logical Axioms: 16]Includes Ontology(OntologyID(OntologyIRI(<http://purl.obolibrary.org/obo/uberon/bridge/uberon-bridge-to-xao.owl>) VersionIRI(<http://purl.obolibrary.org/obo/uberon/bridge/uberon-bridge-to-xao/2018-11-25/uberon/bridge/uberon-bridge-to-xao.owl>))) [Axioms: 3144 Logical Axioms: 609]Includes Ontology(OntologyID(OntologyIRI(<http://purl.obolibrary.org/obo/uberon/bridge/uberon-bridge-to-zfa.owl>) VersionIRI(<http://purl.obolibrary.org/obo/uberon/bridge/uberon-bridge-to-zfa/2018-11-25/uberon/bridge/uberon-bridge-to-zfa.owl>))) [Axioms: 10463 Logical Axioms: 2071]Includes Ontology(OntologyID(OntologyIRI(<http://purl.obolibrary.org/obo/uberon/ext.owl>) VersionIRI(<http://purl.obolibrary.org/obo/uberon/releases/2018-11-25/ext.owl>))) [Axioms: 268381 Logical Axioms: 59509]Includes Ontology(OntologyID(OntologyIRI(<http://purl.obolibrary.org/obo/uberon/ssso-merged-uberon.owl>) VersionIRI(<null>))) [Axioms: 10143 Logical Axioms: 3193]Includes Ontology(OntologyID(OntologyIRI(<http://purl.obolibrary.org/obo/wbbt.owl>) VersionIRI(<http://purl.obolibrary.org/obo/wbbt/2015-04-03/wbbt.owl>))) [Axioms: 36258 Logical Axioms: 12383]Includes Ontology(OntologyID(OntologyIRI(<http://purl.obolibrary.org/obo/wbls.owl>) VersionIRI(<http://purl.obolibrary.org/obo/wbls/releases/2015-04-15/wbls.owl>))) [Axioms: 3399 Logical Axioms: 1345]Includes Ontology(OntologyID(OntologyIRI(<http://purl.obolibrary.org/obo/xao.owl>) VersionIRI(<http://purl.obolibrary.org/obo/xao/2013-10-09/xao.owl>))) [Axioms: 10054 Logical Axioms: 5157]Includes Ontology(OntologyID(OntologyIRI(<http://purl.obolibrary.org/obo/zfa.owl>) VersionIRI(<http://purl.obolibrary.org/obo/zfa/releases/2014-09-12/zfa.owl>))) [Axioms: 22468 Logical Axioms: 11339]http://genomebiology.com/2012/13/1/R5http://purl.obolibrary.org/obo/uberon/references/reference_0000027http://purl.obolibrary.org/obo/uberon/bridge/collected-metazoahttp://uberon.orgIAO:0000112uberontrueexample_of_usageexample of usagedefinitionIAO:0000116uberontrueeditor_noteeditor noteeditor noteIAO:0000122trueexample_of_usageexample of usageIAO:0000232uberontruecurator_notescurator notesexpand expression toexpand assertion toterm replaced byS never_in_taxon T iff: S SubClassOf in_taxon only not TClass: <http://www.w3.org/2002/07/owl#Nothing> EquivalentTo: ?X and (RO_0002162 some ?Y)RO:0002161uberontruetruenever_in_taxonnever_in_taxonS never_in_taxon T iff: S SubClassOf in_taxon only not TClass: <http://www.w3.org/2002/07/owl#Nothing> EquivalentTo: (BFO_0000050 some ?X) and (BFO_0000050 some ?Y)RO:0002171uberontruetruemutually_spatially_disjoint_withmutually_spatially_disjoint_withS ambiguous_for_taxon T if the class S does not have a clear referent in taxon T. An example would be the class 'manual digit 1', which encompasses a homology hypotheses that is accepted for some species (e.g. human and mouse), but does not have a clear referent in Aves - the referent is dependent on the hypothesis embraced, and also on the ontogenetic stage.RO:0002173uberontruetrueambiguous_for_taxonambiguous_for_taxonS ambiguous_for_taxon T if the class S does not have a clear referent in taxon T. An example would be the class 'manual digit 1', which encompasses a homology hypotheses that is accepted for some species (e.g. human and mouse), but does not have a clear referent in Aves - the referent is dependent on the hypothesis embraced, and also on the ontogenetic stage.PHENOSCPAE:asilomar_mtgS dubious_for_taxon T if it is probably the case that no instances of S can be found in any instance of T.RO:0002174uberontruetruedubious_for_taxonthis relation lacks a strong logical interpretation, but can be used in place of never_in_taxon where it is desirable to state that the definition of the class is too strict for the taxon under consideration, but placing a never_in_taxon link would result in a chain of inconsistencies that will take time to resolve. Example: metencephalon in teleostdubious_for_taxonS dubious_for_taxon T if it is probably the case that no instances of S can be found in any instance of T.S present_in_taxon T if some instance of T has some S. This does not means that all instances of T have an S - it may only be certain life stages or sexes that have SRO:0002175applicable for taxonuberontruetruepresent_in_taxonpresent_in_taxonS present_in_taxon T if some instance of T has some S. This does not means that all instances of T have an S - it may only be certain life stages or sexes that have SA is has_no_connections_with B if there are no parts of A or B that have a connection with the other.Class: <http://www.w3.org/2002/07/owl#Nothing> EquivalentTo: (BFO_0000050 some ?X) and (RO_0002170 some (BFO_0000050 some ?Y))RO:0002475uberontruetruehas_no_connections_withhas_no_connections_withA is has_no_connections_with B if there are no parts of A or B that have a connection with the other.If R <- P o Q is a defining property chain axiom, then it also holds that R -> P o Q. Note that this cannot be expressed directly in OWLis a defining property chain axiomIf R <- P o Q is a defining property chain axiom, then (1) R -> P o Q holds and (2) Q is either reflexive or locally reflexive. A corollary of this is that P SubPropertyOf R.is a defining property chain axiom where second argument is reflexiveAn alternate textual definition for a class taken unmodified from an external source. This definition may have been used to derive a generalized definition for the new class.UBPROP:0000001uberontrueexternal_definitionThis annotation property may be replaced with an annotation property from an external ontology such as IAOexternal_definitionAn alternate textual definition for a class taken unmodified from an external source. This definition may have been used to derive a generalized definition for the new class.A textual description of an axiom loss in this ontology compared to an external ontology.UBPROP:0000002uberontrueaxiom_lost_from_external_ontologyThis annotation property may be replaced with an annotation property from an external ontology such as IAOaxiom_lost_from_external_ontologyA textual description of an axiom loss in this ontology compared to an external ontology.Notes on the homology status of this class.UBPROP:0000003uberontruehomology_notesThis annotation property may be replaced with an annotation property from an external ontology such as IAOhomology_notesNotes on the homology status of this class.An alternate comment for a class taken unmodified from an external source. Note that obo format only allows a single comment for a class, and does not provide a structured means of adding provenance info.UBPROP:0000005uberontrueexternal_commentThis annotation property may be replaced with an annotation property from an external ontology such as IAOexternal_commentAn alternate comment for a class taken unmodified from an external source. Note that obo format only allows a single comment for a class, and does not provide a structured means of adding provenance info.UBPROP:0000006uberontrueimplements_design_patternimplements_design_patternUsed to connect a class to an adjectival form of its label. For example, a class with label 'intestine' may have a relational adjective 'intestinal'.UBPROP:0000007uberontruehas_relational_adjectiveUsed to connect a class to an adjectival form of its label. For example, a class with label 'intestine' may have a relational adjective 'intestinal'.has_relational_adjectiveNotes on the how instances of this class vary across species.UBPROP:0000008uberontruetaxon_notestaxon_notesNotes on the how instances of this class vary across species.Notes on the evolved function of instances of this class.This annotation property may be replaced with an annotation property from an external ontology such as IAOUBPROP:0000009uberontruefunction_notesfunction_notesNotes on the evolved function of instances of this class.Notes on the structure, composition or histology of instances of this class.This annotation property may be replaced with an annotation property from an external ontology such as IAOUBPROP:0000010uberontruestructure_notesstructure_notesNotes on the structure, composition or histology of instances of this class.Notes on the ontogenic development of instances of this class.This annotation property may be replaced with an annotation property from an external ontology such as IAOUBPROP:0000011uberontruedevelopment_notesdevelopment_notesNotes on the ontogenic development of instances of this class.Notes on how similar or equivalent classes are represented in other ontologies.This annotation property may be replaced with an annotation property from an external ontology such as IAOUBPROP:0000012uberontrueexternal_ontology_notesexternal_ontology_notesNotes on how similar or equivalent classes are represented in other ontologies.Notes on how lexical conventions regarding this class, in particular any issues that may arise due to homonyny or synonymy.This annotation property may be replaced with an annotation property from an external ontology such as IAOUBPROP:0000013uberontrueterminology_notesterminology_notesNotes on how lexical conventions regarding this class, in particular any issues that may arise due to homonyny or synonymy.Notes on how instances of this class functon biomechanically.This annotation property may be replaced with an annotation property from an external ontology such as IAOUBPROP:0000014uberontrueaction_notesactions_notesNotes on how instances of this class functon biomechanically.Notes on the location, position or part-parents of instances of this class.This annotation property may be replaced with an annotation property from an external ontology such as IAOUBPROP:0000015uberontruelocation_noteslocation_notesNotes on the location, position or part-parents of instances of this class.UBPROP:0000100uberontrueis_count_ofis count ofA property used in conjunction with repeated_element_number to indicate an axis and directionality along that axis. If P preceding_element_is R, and P is_count_of S, and X P N, and X' P N+1, then it follows that every X R some X', and the class expression [S and R some X' and inv(R) some X] is empty (i.e. X is followed by X', with no intermediates)UBPROP:0000101uberontruepreceding_element_ispreceding element isA property used in conjunction with repeated_element_number to indicate an axis and directionality along that axis. If P preceding_element_is R, and P is_count_of S, and X P N, and X' P N+1, then it follows that every X R some X', and the class expression [S and R some X' and inv(R) some X] is empty (i.e. X is followed by X', with no intermediates)A property used to indicate the position of an element where that element is of a type that is serially repeated linearly along some axis for which a total ordering exists. The ordering may represent an ancestral conditionUBPROP:0000102uberontruerepeated_element_numberThe range is currently non-negative integerrepeated element numberA property used to indicate the position of an element where that element is of a type that is serially repeated linearly along some axis for which a total ordering exists. The ordering may represent an ancestral conditionx pharyngeal_arch_number N if and only if (i) x is a pharyngeal arch, and (ii) x is ancestrally pharyngeal arch number N in a series of pharyngeal arches repeated along a antero-posterior axis, with arch_number 1 being the mandibular arch.gill arch N = PA N-2. the term branchial_arch is ambiguous.UBPROP:0000103uberontruepharyngeal_arch_numberpharyngeal arch numberx pharyngeal_arch_number N if and only if (i) x is a pharyngeal arch, and (ii) x is ancestrally pharyngeal arch number N in a series of pharyngeal arches repeated along a antero-posterior axis, with arch_number 1 being the mandibular arch.x ray_number N if and only if (i) x is a ray, and (ii) x is ancestrally associated with ray number N in a series of phalanges repeated along a radio-ulnar or equivalent axis, with ray_number 1 being the anteriormost ray.UBPROP:0000104uberontrueray_numberThe correct terminology is yet to be established; in tetrapods 'ray' might mean the mereological sum of the phalanges of a manual digit plus a metatarsal bone (or equivalent for hindlimb)ray numberx ray_number N if and only if (i) x is a ray, and (ii) x is ancestrally associated with ray number N in a series of phalanges repeated along a radio-ulnar or equivalent axis, with ray_number 1 being the anteriormost ray.x phalanx_number N if and only if (i) x is a phalanx, and (ii) x is phalanx number N in a series of phalanges repeated along an prixomo-distal axis, with phalanx_number 1 being the proximalmost phalanx. Note that in humans, the distalmost phalanx has phlanax_number 3, except in ray_number 1, where the distalmost has phalanx_number 2UBPROP:0000105uberontruephalanx_numberMost land mammals including humans have a 2-3-3-3-3 formula in both the hands (or paws) and feet. Primitive reptiles typically had the formula 2-3-4-4-5, and this pattern, with some modification, remained in many later reptiles and in the mammal-like reptiles. The phalangeal formula in the flippers of cetaceans (marine mammals) is 2-12-8-1phalanx numberx phalanx_number N if and only if (i) x is a phalanx, and (ii) x is phalanx number N in a series of phalanges repeated along an prixomo-distal axis, with phalanx_number 1 being the proximalmost phalanx. Note that in humans, the distalmost phalanx has phlanax_number 3, except in ray_number 1, where the distalmost has phalanx_number 2x rib_number N if and only if (i) x is a rib, and (ii) x is rib number N in a series of ribs repeated along an anterior-posterior axis, with rib_number 1 being the anteriormost rib. Note that this property counts ribs, *not* the adjoining vertebrae.In the early tetrapods, every vertebra bore a pair of ribs, although those on the thoracic vertebrae are typically the longest. In most subsequent forms, many of these early ribs have been lost, and in living amphibians and reptiles, there is great variation in rib structure and number. For example, turtles have only eight pairs of ribs, which are developed into a bony or cartilagenous carapace and plastron, while snakes have numerous ribs running along the full length of their trunk. Frogs typically have no ribs, aside from a sacral pair, which form part of the pelvis. Mammals usually also only have distinct ribs on the thoracic vertebra, although fixed cervical ribs are also present in monotremes. In marsupials and placental mammals, the cervical and lumbar ribs are found only as tiny remnants fused to the vertebrae, where they are referred to as transverse processes. In general, the structure and number of the true ribs in humans is similar to that in other mammals. Unlike reptiles, caudal ribs are never found in mammals.Note that in TAO, ribs are numbered by *vertebrae*UBPROP:0000106uberontruerib_numberrib numberx rib_number N if and only if (i) x is a rib, and (ii) x is rib number N in a series of ribs repeated along an anterior-posterior axis, with rib_number 1 being the anteriormost rib. Note that this property counts ribs, *not* the adjoining vertebrae.Note that in TAO, ribs are numbered by *vertebrae*TAOx vertebra_number N if and only if (i) x is a vertebra, and (ii) x is vertebra number N in a series of vertebras repeated along an anterior-posterior axis, with vertebra_number 1 being the anteriormost vertebra (also known as the atlas).UBPROP:0000107uberontruevertebra_numbervertebra numberx vertebra_number N if and only if (i) x is a vertebra, and (ii) x is vertebra number N in a series of vertebras repeated along an anterior-posterior axis, with vertebra_number 1 being the anteriormost vertebra (also known as the atlas).x somite_number N if and only if (i) x is a somite, and (ii) x is somite number N in a series of somites repeated along an anterior-posterior axis, with somite_number 1 being the anteriormost somite.UBPROP:0000108uberontruesomite_numbersomite numberx somite_number N if and only if (i) x is a somite, and (ii) x is somite number N in a series of somites repeated along an anterior-posterior axis, with somite_number 1 being the anteriormost somite.x paired_appendage_number N if and only if (i) x is a paired_appendage, and (ii) x is paired_appendage number N in a series of paired_appendages repeated along an anterior-posterior axis, with paired_appendage_number 1 being the anteriormost paired_appendage. In vertebrates, this is the pectoral appendageUBPROP:0000109uberontruepaired_appendage_numberpaired_appendage numberx paired_appendage_number N if and only if (i) x is a paired_appendage, and (ii) x is paired_appendage number N in a series of paired_appendages repeated along an anterior-posterior axis, with paired_appendage_number 1 being the anteriormost paired_appendage. In vertebrates, this is the pectoral appendagex appendage_segment_number N if and only if (i) x is a appendage_segment, and (ii) x is appendage_segment number N in a series of appendage_segments repeated along an proximo-distal axis, with appendage_segment_number 1 being the proximalmost appendage_segment (in tetrapods this would be the stylopod, as we do not classify girdles as appendage segments).UBPROP:0000110uberontrueappendage_segment_numberExamples: in dropsphila coxa=1, trochanter=2, femur=3, tibia=4, tarsal segments 1-5=5-9, pretarsus=10appendage segment numberx appendage_segment_number N if and only if (i) x is a appendage_segment, and (ii) x is appendage_segment number N in a series of appendage_segments repeated along an proximo-distal axis, with appendage_segment_number 1 being the proximalmost appendage_segment (in tetrapods this would be the stylopod, as we do not classify girdles as appendage segments).x rhombomere_number N if and only if (i) x is a rhombomere, and (ii) x is rhombomere number N in a series of rhombomeres repeated along an anterior-posterior axis, with rhombomere_number 1 being the anteriormost rhombomere.UBPROP:0000111uberontruerhombomere_numberrhombomere numberx rhombomere_number N if and only if (i) x is a rhombomere, and (ii) x is rhombomere number N in a series of rhombomeres repeated along an anterior-posterior axis, with rhombomere_number 1 being the anteriormost rhombomere.x tooth_number N if and only if (i) x is a tooth, and (ii) x is ancestrally tooth number N in a series of teeth repeated along an anterior-posterior axis, typically on the lateral side of a structure such as a jaw, with tooth_number 1 being the anteriormost. Note that this count refers to the total number of teeth starting from the first, regardless of the type of tooth. If sub-systems are required for numbering within a series of teeth of the same type, consider a subproperty. For example, in a human, maxillary canine = tooth 3 of upper jaw = canine_tooth 1 of upper jawUBPROP:0000112uberontruetooth_numbertooth numberSyntax: upper/lower = I.C.P.M / I.C.P.M. When used with generic tooth class applies to both deciduous and primary. Should also be used with a taxon property.UBPROP:0000113uberontruedental_formuladental formulaSyntax: upper/lower = I.C.P.M / I.C.P.M. When used with generic tooth class applies to both deciduous and primary. Should also be used with a taxon property.UBPROP:0000201uberontruesource_atlassource atlasFMA has terms like 'set of X'. In general we do not include set-of terms in uberon, but provide a mapping between the singular form and the FMA set termUBPROP:0000202uberontruefma_set_termfma_set_termFMA has terms like 'set of X'. In general we do not include set-of terms in uberon, but provide a mapping between the singular form and the FMA set termFMADefines the start and end of a stage with a duration of 1 month, relative to either the time of fertilization or last menstrual period of the mother (to be clarified), counting from one, in terms of a reference model. Thus if month_of_gestation=3, then the stage is 2 month in.Wikipedia:Gestational_agehuman_stages_ontologytruemonth_of_gestationThis is a shortcut annotation that can be expanded to an OWL axiom, or to a set of OWL axioms. The exact translation has yet to be determined, and may be application-dependent.month of gestationpreferred term when talking about an instance of this class in Homo sapienslatin termplural termabbreviationabbreviationabbreviationabbreviationabbreviationabbreviationpreferred term in the context of comparative anatomyA historic synonym, no longer encourageddevelopmental termdubious or contested synonyma synonym made on the basis of a possibly homologous structure in another speciespreferred term when talking about an instance of this class in Homo sapiensindicates that a synonym is used in an inconsistent or confusing way, typically between specieslatin terma mis-spelling that is in common use and thus recordedsynonym that is inappropriate for amniotessynonym that is inappropriate for mammalsexpert consultation and attribution requiredplural termtaxonomic disambiguationa systematic synonym used as the base name for design patternsCUMBOcyclostome structuresbrain region defined by cyto-architectureclasses that are defined by relative position counting from first in a series of elements along an axis in an individual organism rather than by strict homologydevelopmental_classificationIndicates that subclasses in AOs may be inappropriately linkedA class that represents an early developmental structure, like a blastocyst. This part of the ontology is undergoing review to remove inappropriate grouping classes.EFO slimderived from the union of EHDAA2 and EMAPA - still to be checkedsubset of classes that have logical defs text defs and synonyms aligned with FEEDfunctional_classificationSubset consisting of classes creating for grouping purposesuberontrueStatus: experimentalhomologous_inA grouping class that depends on an assumption of homology between subclassesclasses that have some inconsistency with FMAsomewhat fuzzy grouping for analysis purposes, currently composed of something like: liver, heart, skeletal, kidney, bladder, brain, skin, mouth, esophagus, stomach, small intestine, large intestines, trachea nose, lungs, brain, spinal cord, peripheral nerves, kidneys, ureters, bladder, urethra, gonadscore classes typically found across metazoa. one purpose is to create a rough set of terms that could be used to start a new metazoan AO. Note this subset is not yet fully fleshed outabstract class brought in to group ontology classes but not informativeorgans, excluding individual muscles and skeletal elementsPhenotype slimA subset specifically created for the 2012 Phenotype RCN meeting. Includes some human-specific terms that may eventually be removed when they are adequately represented with part of relationships in FMAUberon slim - subset that excludes obscure terms and deep compositional termsIndicates that the class encompasses classes from other AOs that have not been verifiedabstract upper-level terms not directly useful for analysiscore classes typically found across vertebrates. one purpose is to create a rough set of terms that could be used to start a new vertebrate AOpluralsEFO slimCount of number of days intervening between the end of the stage and the time of birth according to a reference model. Note that the first day of post-birth development has the value of 1 for this property, and the period during which the child is one day old has the value 2cat_stages_ontologycavy_stages_ontologydog_stages_ontologyhedgehog_stages_ontologyrabbit_stages_ontologytrueThis is a shortcut annotation that can be expanded to an OWL axiom, or to a set of OWL axioms. The exact translation has yet to be determined, and may be application-dependent.end, days post birthCount of number of days intervening between the end of the stage and the time of coitum, assuming that it takes place around midnight during a 7pm to 5am dark cycle (noon of the day on which the vaginal plug is found, the embryos are aged 0.5 days post coitum).Count of number of days intervening between the end of the stage and the time of coitum, defined as the time the vaginal plug is found. Note that the vaginal plug persists for 16-24 hours and may lasts as long as 48 hours.mouse_stages_ontologyrat_stages_ontologytrueThis is a shortcut annotation that can be expanded to an OWL axiom, or to a set of OWL axioms. The exact translation has yet to be determined, and may be application-dependent.end, days post coitumCount of number of days intervening between the end of the stage and the time of coitum, assuming that it takes place around midnight during a 7pm to 5am dark cycle (noon of the day on which the vaginal plug is found, the embryos are aged 0.5 days post coitum).http://php.med.unsw.edu.au/embryology/index.php?title=Mouse_Stages#Timed_PregnancyCount of number of days intervening between the end of the stage and the time of coitum, defined as the time the vaginal plug is found. Note that the vaginal plug persists for 16-24 hours and may lasts as long as 48 hours.http://web.jhu.edu/animalcare/procedures/rat.htmlCount of number of days intervening between the end of the stage and the time of fertilization according to a reference model. Note that the first day of development has the value of 1 for this property.bonobo_stages_ontologycat_stages_ontologycavy_stages_ontologychicken_stages_ontologychimpanzee_stages_ontologycow_stages_ontologydog_stages_ontologygorilla_stages_ontologyhedgehog_stages_ontologyhorse_stages_ontologyhuman_stages_ontologylizard_stages_ontologyopossum_stages_ontologyorangutan_stages_ontologypig_stages_ontologyplatypus_stages_ontologypufferfish_stages_ontologyrabbit_stages_ontologyrhesus_macaque_stages_ontologytrueThis is a shortcut annotation that can be expanded to an OWL axiom, or to a set of OWL axioms. The exact translation has yet to be determined, and may be application-dependent.end, days post fertilizationCount of number of days intervening between the end of the stage and the time of hatching according to a reference model. Note that the first day of post-birth development has the value of 1 for this property, and the period during which the organism is one day old has the value 2.Dananassae_stages_ontologyDmojavensis_stages_ontologyDpseudobscura_stages_ontologyDsimulans_stages_ontologyDvirilis_stages_ontologyDyakuba_stages_ontologytrueThis is a shortcut annotation that can be expanded to an OWL axiom, or to a set of OWL axioms. The exact translation has yet to be determined, and may be applirabbition-dependent.end, days post hatchingCount of number of months intervening between the end of the stage and the time of birth according to a reference model. Note that the first month of post-birth development has the value of 1 for this property, and the period during which the child is one month old has the value 2Count of number of months intervening between the end of the stage and the time of birth according to a reference model. Note that the first month of post-birth development has the value of 1 for this property, and the period during which the mouse is one month old has the value 2Count of number of months intervening between the end of the stage and the time of birth according to a reference model. Note that the first month of post-birth development has the value of 1 for this property, and the period during which the organism is one month old has the value 2bonobo_stages_ontologycat_stages_ontologycavy_stages_ontologycow_stages_ontologydog_stages_ontologyhedgehog_stages_ontologyhorse_stages_ontologyhuman_stages_ontologymouse_stages_ontologyopossum_stages_ontologyorangutan_stages_ontologypig_stages_ontologyplatypus_stages_ontologyrabbit_stages_ontologyrat_stages_ontologyrhesus_macaque_stages_ontologytrueThis is a shortcut annotation that can be expanded to an OWL axiom, or to a set of OWL axioms. The exact translation has yet to be determined, and may be application-dependent.end, months post birthCount of number of months intervening between the end of the stage and the time of fertilization according to a reference model. Note that the first month of development has the value of 1 for this property, and the period during which the organism is one month old has the value 2bonobo_stages_ontologychimpanzee_stages_ontologycow_stages_ontologygorilla_stages_ontologyorangutan_stages_ontologypig_stages_ontologyrhesus_macaque_stages_ontologytrueThis is a shortcut annotation that can be expanded to an OWL axiom, or to a set of OWL axioms. The exact translation has yet to be determined, and may be application-dependent.end, months post fertilizationCount of number of months intervening between the end of the stage and the time of hatching according to a reference model. Note that the first month of post-birth development has the value of 1 for this property, and the period during which the organism is one month old has the value 2chicken_stages_ontologylizard_stages_ontologytrueThis is a shortcut annotation that can be expanded to an OWL axiom, or to a set of OWL axioms. The exact translation has yet to be determined, and may be application-dependent.end, months post hatchingCount of number of weeks intervening between the end of the stage and the time of birth according to a reference model. Note that the first week of post-birth development has the value of 1 for this property, and the period during which the mouse is one week old has the value 2Count of number of weeks intervening between the end of the stage and the time of birth according to a reference model. Note that the first week of post-birth development has the value of 1 for this property, and the period during which the rat is one week old has the value 2mouse_stages_ontologyopossum_stages_ontologyplatypus_stages_ontologyrat_stages_ontologytrueThis is a shortcut annotation that can be expanded to an OWL axiom, or to a set of OWL axioms. The exact translation has yet to be determined, and may be application-dependent.end, weeks post birthCount of number of years intervening between the end of the stage and the time of birth according to a reference model. Note that the first year of post-birth development has the value of 1 for this property, and the period during which the child is one year old has the value 2bonobo_stages_ontologycat_stages_ontologycavy_stages_ontologychimpanzee_stages_ontologycow_stages_ontologydog_stages_ontologygorilla_stages_ontologyhedgehog_stages_ontologyhorse_stages_ontologyhuman_stages_ontologyorangutan_stages_ontologypig_stages_ontologyrabbit_stages_ontologyrhesus_macaque_stages_ontologytrueThis is a shortcut annotation that can be expanded to an OWL axiom, or to a set of OWL axioms. The exact translation has yet to be determined, and may be application-dependent.end, years post birthCount of number of years intervening between the end of the stage and the time of hatching according to a reference model. Note that the first year of post-birth development has the value of 1 for this property, and the period during which the organism is one year old has the value 2pufferfish_stages_ontologytrueThis is a shortcut annotation that can be expanded to an OWL axiom, or to a set of OWL axioms. The exact translation has yet to be determined, and may be application-dependent.end, years post hatchingSubset consisting of classes describing highly granular developmental stages (for instance, '23-year-old'). Such stages might be useful for annotation purpose, but might be folded into less granular parents for display purpose.Dananassae_stages_ontologyDmojavensis_stages_ontologyDpseudobscura_stages_ontologyDsimulans_stages_ontologyDvirilis_stages_ontologyDyakuba_stages_ontologybonobo_stages_ontologycat_stages_ontologycavy_stages_ontologychicken_stages_ontologychimpanzee_stages_ontologycow_stages_ontologydog_stages_ontologygorilla_stages_ontologyhedgehog_stages_ontologyhorse_stages_ontologyhuman_stages_ontologylizard_stages_ontologymouse_stages_ontologyopossum_stages_ontologyorangutan_stages_ontologypig_stages_ontologyplatypus_stages_ontologypufferfish_stages_ontologyrabbit_stages_ontologyrat_stages_ontologyrhesus_macaque_stages_ontologytruehas end timeA relationship between a stage class and an anatomical structure or developmental process class, in which the stage is characterized by the appearance of the structure or the occurrence of the biological processhuman_stages_ontologytrueThis is a shortcut annotation that can be expanded to an OWL axiom, or to a set of OWL axioms. The exact translation has yet to be determined, and may be application-dependent.has stage markerDananassae_stages_ontologyDmojavensis_stages_ontologyDpseudobscura_stages_ontologyDsimulans_stages_ontologyDvirilis_stages_ontologyDyakuba_stages_ontologybonobo_stages_ontologycat_stages_ontologycavy_stages_ontologychicken_stages_ontologychimpanzee_stages_ontologycow_stages_ontologydog_stages_ontologygorilla_stages_ontologyhedgehog_stages_ontologyhorse_stages_ontologyhuman_stages_ontologylizard_stages_ontologymouse_stages_ontologyopossum_stages_ontologyorangutan_stages_ontologypig_stages_ontologyplatypus_stages_ontologypufferfish_stages_ontologyrabbit_stages_ontologyrat_stages_ontologyrhesus_macaque_stages_ontologytruehas start timeDananassae_stages_ontologyDmojavensis_stages_ontologyDpseudobscura_stages_ontologyDsimulans_stages_ontologyDvirilis_stages_ontologyDyakuba_stages_ontologybonobo_stages_ontologycat_stages_ontologycavy_stages_ontologychicken_stages_ontologychimpanzee_stages_ontologycow_stages_ontologydog_stages_ontologygorilla_stages_ontologyhedgehog_stages_ontologyhorse_stages_ontologyhuman_stages_ontologylizard_stages_ontologymouse_stages_ontologyopossum_stages_ontologyorangutan_stages_ontologypig_stages_ontologyplatypus_stages_ontologypufferfish_stages_ontologyrabbit_stages_ontologyrat_stages_ontologyrhesus_macaque_stages_ontologytrueUsed to associate a measurement property (e.g. days post fertilization) with a unit (e.g. days)has unitCount of number of days intervening between the start of the stage and the time of birth according to a reference model. Note that the first day of post-birth development has the value of 0 for this property, and the period during which the child is one day old has the value 1.cat_stages_ontologycavy_stages_ontologydog_stages_ontologyhedgehog_stages_ontologyrabbit_stages_ontologytrueThis is a shortcut annotation that can be expanded to an OWL axiom, or to a set of OWL axioms. The exact translation has yet to be determined, and may be application-dependent.start, days post birthCount of number of days intervening between the start of the stage and the time of coitum, assuming that it takes place around midnight during a 7pm to 5am dark cycle (noon of the day on which the vaginal plug is found, the embryos are aged 0.5 days post coitum).Count of number of days intervening between the start of the stage and the time of coitum, defined as the time the vaginal plug is found. Note that the vaginal plug persists for 16-24 hours and may lasts as long as 48 hours.mouse_stages_ontologyrat_stages_ontologytrueThis is a shortcut annotation that can be expanded to an OWL axiom, or to a set of OWL axioms. The exact translation has yet to be determined, and may be application-dependent.start, days post coitumCount of number of days intervening between the start of the stage and the time of coitum, assuming that it takes place around midnight during a 7pm to 5am dark cycle (noon of the day on which the vaginal plug is found, the embryos are aged 0.5 days post coitum).http://php.med.unsw.edu.au/embryology/index.php?title=Mouse_Stages#Timed_PregnancyCount of number of days intervening between the start of the stage and the time of coitum, defined as the time the vaginal plug is found. Note that the vaginal plug persists for 16-24 hours and may lasts as long as 48 hours.http://web.jhu.edu/animalcare/procedures/rat.htmlCount of number of days intervening between the start of the stage and the time of fertilization according to a reference model. Note that the first day of development has the value of 0 for this property.bonobo_stages_ontologycat_stages_ontologycavy_stages_ontologychicken_stages_ontologychimpanzee_stages_ontologycow_stages_ontologydog_stages_ontologygorilla_stages_ontologyhedgehog_stages_ontologyhorse_stages_ontologyhuman_stages_ontologylizard_stages_ontologymouse_stages_ontologyopossum_stages_ontologyorangutan_stages_ontologypig_stages_ontologyplatypus_stages_ontologypufferfish_stages_ontologyrabbit_stages_ontologyrat_stages_ontologyrhesus_macaque_stages_ontologytrueThis is a shortcut annotation that can be expanded to an OWL axiom, or to a set of OWL axioms. The exact translation has yet to be determined, and may be application-dependent.start, days post fertilizationCount of number of days intervening between the start of the stage and the time of hatching according to a reference model. Note that the first day of post-birth development has the value of 0 for this property, and the period during which the organism is one day old has the value 1.Dananassae_stages_ontologyDmojavensis_stages_ontologyDpseudobscura_stages_ontologyDsimulans_stages_ontologyDvirilis_stages_ontologyDyakuba_stages_ontologytrueThis is a shortcut annotation that can be expanded to an OWL axiom, or to a set of OWL axioms. The exact translation has yet to be determined, and may be application-dependent.start, days post hatchingCount of number of months intervening between the start of the stage and the time of birth according to a reference model. Note that the first month of post-birth development has the value of 0 for this property, and the period during which the child is one month old has the value 1.Count of number of months intervening between the start of the stage and the time of birth according to a reference model. Note that the first month of post-birth development has the value of 0 for this property, and the period during which the mouse is one month old has the value 1.Count of number of months intervening between the start of the stage and the time of birth according to a reference model. Note that the first month of post-birth development has the value of 0 for this property, and the period during which the organism is one month old has the value 1.bonobo_stages_ontologycat_stages_ontologycavy_stages_ontologycow_stages_ontologydog_stages_ontologyhedgehog_stages_ontologyhorse_stages_ontologyhuman_stages_ontologymouse_stages_ontologyopossum_stages_ontologyorangutan_stages_ontologypig_stages_ontologyplatypus_stages_ontologyrabbit_stages_ontologyrat_stages_ontologyrhesus_macaque_stages_ontologytrueThis is a shortcut annotation that can be expanded to an OWL axiom, or to a set of OWL axioms. The exact translation has yet to be determined, and may be application-dependent.start, months post birthCount of number of months intervening between the start of the stage and the time of fertilization according to a reference model. Note that the first month of development has the value of 1 for this property, and the period during which the organism is one month old has the value 1.bonobo_stages_ontologychimpanzee_stages_ontologycow_stages_ontologygorilla_stages_ontologyorangutan_stages_ontologypig_stages_ontologyrhesus_macaque_stages_ontologytrueThis is a shortcut annotation that can be expanded to an OWL axiom, or to a set of OWL axioms. The exact translation has yet to be determined, and may be application-dependent.start, months post fertilizationCount of number of months intervening between the start of the stage and the time of hatching according to a reference model. Note that the first month of post-birth development has the value of 0 for this property, and the period during which the organism is one month old has the value 1.chicken_stages_ontologylizard_stages_ontologytrueThis is a shortcut annotation that can be expanded to an OWL axiom, or to a set of OWL axioms. The exact translation has yet to be determined, and may be application-dependent.start, months post hatchingCount of number of weeks intervening between the start of the stage and the time of birth according to a reference model. Note that the first week of post-birth development has the value of 0 for this property, and the period during which the mouse is one week old has the value 1.Count of number of weeks intervening between the start of the stage and the time of birth according to a reference model. Note that the first week of post-birth development has the value of 0 for this property, and the period during which the rat is one week old has the value 1.mouse_stages_ontologyopossum_stages_ontologyplatypus_stages_ontologyrat_stages_ontologytrueThis is a shortcut annotation that can be expanded to an OWL axiom, or to a set of OWL axioms. The exact translation has yet to be determined, and may be application-dependent.start, weeks post birthCount of number of years intervening between the start of the stage and the time of birth according to a reference model. Note that the first year of post-birth development has the value of 0 for this property, and the period during which the child is one year old has the value 1.bonobo_stages_ontologycat_stages_ontologycavy_stages_ontologychimpanzee_stages_ontologycow_stages_ontologydog_stages_ontologygorilla_stages_ontologyhedgehog_stages_ontologyhorse_stages_ontologyhuman_stages_ontologyorangutan_stages_ontologypig_stages_ontologyrabbit_stages_ontologyrhesus_macaque_stages_ontologytrueThis is a shortcut annotation that can be expanded to an OWL axiom, or to a set of OWL axioms. The exact translation has yet to be determined, and may be application-dependent.start, years post birthCount of number of years intervening between the start of the stage and the time of hatching according to a reference model. Note that the first year of post-birth development has the value of 0 for this property, and the period during which the organism is one year old has the value 1.pufferfish_stages_ontologytrueThis is a shortcut annotation that can be expanded to an OWL axiom, or to a set of OWL axioms. The exact translation has yet to be determined, and may be application-dependent.start, years post hatchingabstract upper-level terms not directly useful for analysishttp://purl.org/dc/elements/1.1/contributoruberontruedc-contributorcontributorhttp://purl.org/dc/elements/1.1/creatoruberontruedc-creatorcreatorhttp://purl.org/dc/elements/1.1/descriptionuberontruedc-descriptiondescriptionhttp://purl.org/dc/elements/1.1/publisheruberontruedc-publisherpublisheruberontruedc-rightsrightshttp://purl.org/dc/elements/1.1/sourceuberontruedc-sourcederived from resourcehttp://purl.org/dc/elements/1.1/titleuberontruedc-titletitlehttp://purl.org/dc/terms/isReferencedByuberontruedcterms-isReferencedByis referenced byhttp://purl.org/dc/terms/referencestruedcterms-referencesreferenceshttp://usefulinc.com/ns/doap#GitRepositoryuberontruedoap-GitRepositoryGit repositoryhttp://usefulinc.com/ns/doap#SVNRepositoryuberontruedoap-SVNRepositorySVN repositoryhttp://usefulinc.com/ns/doap#bug-databaseuberontruedoap-bug-databasebug databaseuberontruedoap-mailing-listmailing listhttp://usefulinc.com/ns/doap#wikiuberontruedoap-wikiwikinamespace-id-rulesubset_propertysynonym_type_propertyconsiderhas_alternative_idhas_broad_synonymdatabase_cross_referencehas_exact_synonymhas_narrow_synonymhas_obo_format_versionhas_obo_namespacehas_related_synonymhas_scopehas_synonym_typein_subsetshorthandtreat-xrefs-as-equivalenttreat-xrefs-as-has-subclasstreat-xrefs-as-is_atreat-xrefs-as-reverse-genus-differentiahttp://www.w3.org/2000/01/rdf-schema#seeAlsotrueseeAlsosee alsohttp://xmlns.com/foaf/0.1/depicted_bytruefoaf-depicted_bydepicted_byhttp://xmlns.com/foaf/0.1/homepageuberontruefoaf-homepagehomepageuberontruefoaf-pagepagea core relation that holds between a part and its wholeBFO:0000050OBO_REL:part_ofDananassae_stages_ontologyDmojavensis_stages_ontologyDpseudobscura_stages_ontologyDsimulans_stages_ontologyDvirilis_stages_ontologyDyakuba_stages_ontologyFlyBase development CVbonobo_stages_ontologycat_stages_ontologycavy_stages_ontologychicken_stages_ontologychimpanzee_stages_ontologycow_stages_ontologydog_stages_ontologygorilla_stages_ontologyhedgehog_stages_ontologyhorse_stages_ontologyhuman_stages_ontologylizard_stages_ontologymedaka_ontologymouse_stages_ontologyopossum_stages_ontologyorangutan_stages_ontologypig_stages_ontologyplatypus_stages_ontologypufferfish_stages_ontologyrabbit_stages_ontologyrat_stages_ontologyrhesus_macaque_stages_ontologyuberonpart_ofpart ofpart ofpart_ofa core relation that holds between a whole and its partBFO:0000051uberonhas_parthas parthas parthas_partBFO:0000056uberonparticipates_inparticipates inX preceded_by Y iff: end(Y) before_or_simultaneous_with start(X)x is preceded by y if and only if the time point at which y ends is before or equivalent to the time point at which x starts. Formally: x preceded by y iff ω(y) <= α(x), where α is a function that maps a process to a start point, and ω is a function that maps a process to an end point.djs932009-10-09T10:00:53ZBFO:0000062OBO_REL:preceded_byis preceded bytakes place afterDananassae_stages_ontologyDmojavensis_stages_ontologyDpseudobscura_stages_ontologyDsimulans_stages_ontologyDvirilis_stages_ontologyDyakuba_stages_ontologyFlyBase development CVbonobo_stages_ontologycat_stages_ontologycavy_stages_ontologychicken_stages_ontologychimpanzee_stages_ontologycow_stages_ontologydog_stages_ontologygorilla_stages_ontologyhedgehog_stages_ontologyhorse_stages_ontologyhuman_stages_ontologylizard_stages_ontologymedaka_ontologymouse_stages_ontologyopossum_stages_ontologyorangutan_stages_ontologypig_stages_ontologyplatypus_stages_ontologypufferfish_stages_ontologyrabbit_stages_ontologyrat_stages_ontologyrhesus_macaque_stages_ontologyuberonpreceded_bypreceded bypreceded_byis preceded bySIO:000249takes place afterAllen:precedesx precedes y if and only if the time point at which x ends is before or equivalent to the time point at which y starts. Formally: x precedes y iff ω(x) <= α(y), where α is a function that maps a process to a start point, and ω is a function that maps a process to an end point.BFO:0000063uberonprecedesprecedesprecedesb occurs_in c =def b is a process and c is a material entity or immaterial entity& there exists a spatiotemporal region r and b occupies_spatiotemporal_region r.& forall(t) if b exists_at t then c exists_at t & there exist spatial regions s and s’ where & b spatially_projects_onto s at t& c is occupies_spatial_region s’ at t& s is a proper_continuant_part_of s’ at toccurs in[copied from inverse property 'occurs in'] b occurs_in c =def b is a process and c is a material entity or immaterial entity& there exists a spatiotemporal region r and b occupies_spatiotemporal_region r.& forall(t) if b exists_at t then c exists_at t & there exist spatial regions s and s’ where & b spatially_projects_onto s at t& c is occupies_spatial_region s’ at t& s is a proper_continuant_part_of s’ at tBFO:0000067uberoncontains_processcontains processcontains processtruetruex anterior_to y iff x is further along the antero-posterior axis than y, towards the head. An antero-posterior axis is an axis that bisects an organism from head end to opposite end of body or tail: bearerx anterior_to y iff x is further along the antero-posterior axis than y, towards the head. An antero-posterior axis is an axis that extends through an organism from head end to opposite end of body or tail.cjm2009-07-31T02:15:46ZBSPO:0000096uberonanterior_toanterior_tox anterior_to y iff x is further along the antero-posterior axis than y, towards the head. An antero-posterior axis is an axis that bisects an organism from head end to opposite end of body or tail: bearerx anterior_to y iff x is further along the antero-posterior axis than y, towards the head. An antero-posterior axis is an axis that extends through an organism from head end to opposite end of body or tail.BSPO:cjmx distal_to y iff x is further along the proximo-distal axis than y, towards the appendage tip. A proximo-distal axis extends from tip of an appendage (distal) to where it joins the body (proximal).BSPO:0000097uberondistal_todistal_tox distal_to y iff x is further along the proximo-distal axis than y, towards the appendage tip. A proximo-distal axis extends from tip of an appendage (distal) to where it joins the body (proximal).x distal_to y iff x is further along the proximo-distal axis than y, towards the appendage tip. A proximo-distal axis extends from tip of an appendage (distal) to where it joins the body (proximal).BSPO:cjmx dorsal_to y iff x is further along the dorso-ventral axis than y, towards the back. A dorso-ventral axis is an axis that bisects an organism from back (e.g. spinal column) to front (e.g. belly).x dorsal_to y iff x is further along the dorso-ventral axis than y, towards the back. A dorso-ventral axis is an axis that extends through an organism from back (e.g. spinal column) to front (e.g. belly).BSPO:0000098uberondorsal_todorsal_tox dorsal_to y iff x is further along the dorso-ventral axis than y, towards the back. A dorso-ventral axis is an axis that bisects an organism from back (e.g. spinal column) to front (e.g. belly).x dorsal_to y iff x is further along the dorso-ventral axis than y, towards the back. A dorso-ventral axis is an axis that extends through an organism from back (e.g. spinal column) to front (e.g. belly).BSPO:cjmx posterior_to y iff x is further along the antero-posterior axis than y, towards the body/tail. An antero-posterior axis is an axis that bisects an organism from head end to opposite end of body or tail.x posterior_to y iff x is further along the antero-posterior axis than y, towards the body/tail. An antero-posterior axis is an axis that extends through an organism from head end to opposite end of body or tail.BSPO:0000099caudal_touberonposterior_toposterior_tox posterior_to y iff x is further along the antero-posterior axis than y, towards the body/tail. An antero-posterior axis is an axis that bisects an organism from head end to opposite end of body or tail.x posterior_to y iff x is further along the antero-posterior axis than y, towards the body/tail. An antero-posterior axis is an axis that extends through an organism from head end to opposite end of body or tail.BSPO:cjmx proximal_to y iff x is closer to the point of attachment with the body than y.BSPO:0000100uberonproximal_toproximal_tox proximal_to y iff x is closer to the point of attachment with the body than y.x proximal_to y iff x is closer to the point of attachment with the body than y.BSPO:cjmx ventral_to y iff x is further along the dorso-ventral axis than y, towards the front. A dorso-ventral axis is an axis that bisects an organism from back (e.g. spinal column) to front (e.g. belly).x ventral_to y iff x is further along the dorso-ventral axis than y, towards the front. A dorso-ventral axis is an axis that extends through an organism from back (e.g. spinal column) to front (e.g. belly).BSPO:0000102uberonventral_toventral_tox ventral_to y iff x is further along the dorso-ventral axis than y, towards the front. A dorso-ventral axis is an axis that bisects an organism from back (e.g. spinal column) to front (e.g. belly).x ventral_to y iff x is further along the dorso-ventral axis than y, towards the front. A dorso-ventral axis is an axis that extends through an organism from back (e.g. spinal column) to front (e.g. belly).BSPO:cjmFurther away from the surface of the organism. Thus, the muscular layer is deep to the skin, but superficial to the intestines.BSPO:0000107uberondeep_todeep_toFurther away from the surface of the organism. Thus, the muscular layer is deep to the skin, but superficial to the intestines.Further away from the surface of the organism. Thus, the muscular layer is deep to the skin, but superficial to the intestines.BSPO:cjmNear the outer surface of the organism. Thus, skin is superficial to the muscle layer.BSPO:0000108uberonsuperficial_tosuperficial_toNear the outer surface of the organism. Thus, skin is superficial to the muscle layer.Near the outer surface of the organism. Thus, skin is superficial to the muscle layer.BSPO:cjmX in_left_side_of Y <=> if Y is subdivided into left and right portions, X is part_of the left portion.X in_left_side_of Y <=> if Y is subdivided into two left and right portions, X is part_of the left portion.BSPO:0000120uberonin_left_side_ofin_left_side_ofhttps://github.com/obophenotype/uberon/wiki/Modeling-paired-structures-Design-PatternX in_left_side_of Y <=> if Y is subdivided into left and right portions, X is part_of the left portion.BSPO:PATO_mtg_2009X in_left_side_of Y <=> if Y is subdivided into two left and right portions, X is part_of the left portion.BSPO:PATO_mtg_2009X in_right_side_of Y <=> if Y is subdivided into left and right portions, X is part_of the right portion.X in_right_side_of Y <=> if Y is subdivided into two left and right portions, X is part_of the right portion.BSPO:0000121uberonin_right_side_ofin_right_side_ofhttps://github.com/obophenotype/uberon/wiki/Modeling-paired-structures-Design-PatternX in_right_side_of Y <=> if Y is subdivided into left and right portions, X is part_of the right portion.BSPO:PATO_mtg_2009X in_right_side_of Y <=> if Y is subdivided into two left and right portions, X is part_of the right portion.BSPO:PATO_mtg_2009X posterior_side_of Y <=> if Y is subdivided into two anterior and posterior portions, X is part_of the posterior portion.BSPO:0000122uberonin_posterior_side_ofin_posterior_side_ofX posterior_side_of Y <=> if Y is subdivided into two anterior and posterior portions, X is part_of the posterior portion.BSPO:PATO_mtg_2009X anterior_side_of Y <=> if Y is subdivided into two anterior and posterior portions, X is part_of the anterior portion.BSPO:0000123uberonin_anterior_side_ofin_anterior_side_ofX anterior_side_of Y <=> if Y is subdivided into two anterior and posterior portions, X is part_of the anterior portion.BSPO:PATO_mtg_2009X proximal_side_of Y <=> if Y is subdivided into distal and proximal portions, X is part_of the proximal portion.x in_proximal_side_of y <=> if y is subdivided into two proximal and distal portions, y is part_of the proximal portion.BSPO:0000124uberonin_proximal_side_ofin_proximal_side_ofX proximal_side_of Y <=> if Y is subdivided into distal and proximal portions, X is part_of the proximal portion.BSPO:PATO_mtg_2009x in_proximal_side_of y <=> if y is subdivided into two proximal and distal portions, y is part_of the proximal portion.BSPO:PATO_mtg_2009X distal_side_of Y <=> if Y is subdivided into distal and proximal portions, X is part_of the distal portion.x in_distal_side_of y <=> if y is subdivided into two proximal and distal portions, y is part_of the distal portion.BSPO:0000125uberonin_distal_side_ofin_distal_side_ofX distal_side_of Y <=> if Y is subdivided into distal and proximal portions, X is part_of the distal portion.BSPO:PATO_mtg_2009x in_distal_side_of y <=> if y is subdivided into two proximal and distal portions, y is part_of the distal portion.BSPO:PATO_mtg_2009X in_lateral_side_of Y <=> if X is in_left_side_of Y or X is in_right_side_of Y. X is often, but not always a paired structureBSPO:0000126uberonin_lateral_side_ofin_lateral_side_ofhttps://github.com/obophenotype/uberon/wiki/Modeling-paired-structures-Design-PatternX in_lateral_side_of Y <=> if X is in_left_side_of Y or X is in_right_side_of Y. X is often, but not always a paired structureX in_lateral_side_of Y <=> if X is in_left_side_of Y or X is in_right_side_of Y. X is often, but not always a paired structureUBERON:cjmX superficial_part_of Y <=> if Y is subdivided into two superficial and deep portions, X is part_of the superficial portion.BSPO:0001100uberonin_superficial_part_ofin_superficial_part_ofX superficial_part_of Y <=> if Y is subdivided into two superficial and deep portions, X is part_of the superficial portion.X superficial_part_of Y <=> if Y is subdivided into two superficial and deep portions, X is part_of the superficial portion.BSPO:cjmX superficial_part_of Y <=> if Y is subdivided into two superficial and deep portions, X is part_of the deep portion.BSPO:0001101uberonin_deep_part_ofin_deep_part_ofX superficial_part_of Y <=> if Y is subdivided into two superficial and deep portions, X is part_of the deep portion.X superficial_part_of Y <=> if Y is subdivided into two superficial and deep portions, X is part_of the deep portion.BSPO:cjmX proximalmost_part_of Y <=> X is in_proximal_side_of Y and X is adjacent_to the proximal boundary of YX proximalmost_part_of Y <=> X is part_of Y and X is adjacent_to the proximal boundary of YBSPO:0001106uberonproximalmost_part_ofproximalmost_part_ofX proximalmost_part_of Y <=> X is in_proximal_side_of Y and X is adjacent_to the proximal boundary of Yhttps://orcid.org/0000-0002-6601-2165X proximalmost_part_of Y <=> X is part_of Y and X is adjacent_to the proximal boundary of YThis relation holds when both the deep_to and ajdacent_to relationship similarly hold.x immediately_deep_to y iff x deep_to y and x is contiguous with y.BSPO:0001107uberonimmediately_deep_toimmediately_deep_toThis relation holds when both the deep_to and ajdacent_to relationship similarly hold.x immediately_deep_to y iff x deep_to y and x is contiguous with y.BSPO:curatorsX distalmost_part_of Y <=> X is in_distal_side_of Y and X is adjacent_to the distal boundary of YX distalmost_part_of Y <=> X is part_of Y and X is adjacent_to the distal boundary of YBSPO:0001108uberondistalmost_part_ofdistalmost_part_ofX distalmost_part_of Y <=> X is in_distal_side_of Y and X is adjacent_to the distal boundary of Yhttps://orcid.org/0000-0002-6601-2165X distalmost_part_of Y <=> X is part_of Y and X is adjacent_to the distal boundary of YBSPO:0001113uberonpreaxialmost_part_ofpreaxialmost_part_ofx preaxial_to y iff x is further along the preaxial-postaxial axis than y, towards the postaxial side.BSPO:0001114uberonposterior_to (developmentally)postaxial_topostaxial_tox preaxial_to y iff x is further along the preaxial-postaxial axis than y, towards the postaxial side.posterior_to (developmentally)MA:thBSPO:0001115uberonpostaxialmost_part_ofpostaxialmost_part_ofX intersects_median_plane of iff X crosses the midine plane of Y.BSPO:0005001uberonintersects_midsagittal_plane_ofintersects_midsagittal_plane_ofx immediately_anterior_to y iff x anterior_to y and x is contiguous with y.BSPO:0015009uberonimmediately_anterior_toimmediately_anterior_tox immediately_anterior_to y iff x anterior_to y and x is contiguous with y.BSPO:curatorsx immediately_posterior_to y iff x posterior_to y and x is contiguous with y.BSPO:0015012uberonimmediately_posterior_toimmediately_posterior_tox immediately_posterior_to y iff x posterior_to y and x is contiguous with y.BSPO:curatorsx immediately_superficial_to y iff x superficial_to y and x is contiguous with y.BSPO:0015014uberonimmediately_superficial_toimmediately_superficial_tox immediately_superficial_to y iff x superficial_to y and x is contiguous with y.BSPO:curatorsBSPO:0015101uberonin_dorsal_side_ofin_dorsal_side_ofBSPO:0015102uberonin_ventral_side_ofin_ventral_side_ofnearer to the oral opening of the organism, on the oral-aboral axis.BSPO:0015201uberonoral_tooral_tonearer to the oral opening of the organism, on the oral-aboral axis.BSPO:cjmnearer to the aboral opening of the organism, on the oral-aboral axis.BSPO:0015202uberonaboral_toaboral_tonearer to the aboral opening of the organism, on the oral-aboral axis.BSPO:cjmx preaxial_to y iff x is further along the preaxial-postaxial axis than y, towards the front.BSPO:1000000uberonanterior_to (developmentally)lateral (radial) tomedial (tibial) topreaxial_topreaxial_tox preaxial_to y iff x is further along the preaxial-postaxial axis than y, towards the front.anterior_to (developmentally)MA:tha relation between a specifically dependent continuant (the dependent) and an independent continuant (the bearer), in which the dependent specifically depends on the bearer for its existenceinheres ina relation between an independent continuant (the bearer) and a specifically dependent continuant (the dependent), in which the dependent specifically depends on the bearer for its existenceRO:0000053uberonbearer_ofbearer ofbearer ofa relation between a continuant and a process, in which the continuant is somehow involved in the processparticipates ina relation between a process and a continuant, in which the continuant is somehow involved in the processhas participanta relation between a quality and an independent continuant (the bearer), in which the quality specifically depends on the bearer for its existencequality ofa relation between an independent continuant (the bearer) and a quality, in which the quality specifically depends on the bearer for its existenceRO:0000086uberonhas_qualityhas qualityhas qualitya relation between two independent continuants, the location and the target, in which the target is entirely within the locationRO:0001015uberonlocation_oflocation oflocation_ofcontained inRO:0001019uberoncontainscontainscontainsa relation between two independent continuants, the target and the location, in which the target is entirely within the locationRO:0001025uberonlocated_inlocated inlocated_inThis is redundant with the more specific 'independent and not spatial region' constraint. We leave in the redundant axiom for use with reasoners that do not use negation.This is redundant with the more specific 'independent and not spatial region' constraint. We leave in the redundant axiom for use with reasoners that do not use negation.a relation between a 2D immaterial entity (the boundary) and a material entity, in which the boundary delimits the material entityRO:0002000uberonboundary_of2D boundary ofboundary ofa relation between a material entity and a 2D immaterial entity (the boundary), in which the boundary delimits the material entityRO:0002002uberonhas_boundaryhas 2D boundaryhas boundaryRO:0002005nerve supplyuberoninnervated_byhttp://code.google.com/p/obo-relations/issues/detail?id=6innervated_byinnervated_bynerve supplyFMA:85999X outer_layer_of Y iff:
. X :continuant that bearer_of some PATO:laminar
. X part_of Y
. exists Z :surface
. X has_boundary Z
. Z boundary_of Y
has_boundary: http://purl.obolibrary.org/obo/RO_0002002
boundary_of: http://purl.obolibrary.org/obo/RO_0002000RO:0002007uberonbounding_layer_ofA relationship that applies between a continuant and its outer, bounding layer. Examples include the relationship between a multicellular organism and its integument, between an animal cell and its plasma membrane, and between a membrane bound organelle and its outer/bounding membrane.bounding layer ofbounding layer ofA 'has regulatory component activity' B if A and B are GO molecular functions (GO_0003674), A has_component B and A is regulated by B.has regulatory component activityA relationship that holds between a GO molecular function and a component of that molecular function that negatively regulates the activity of the whole. More formally, A 'has regulatory component activity' B iff :A and B are GO molecular functions (GO_0003674), A has_component B and A is negatively regulated by B.has negative regulatory component activityA relationship that holds between a GO molecular function and a component of that molecular function that positively regulates the activity of the whole. More formally, A 'has regulatory component activity' B iff :A and B are GO molecular functions (GO_0003674), A has_component B and A is positively regulated by B.has positive regulatory component activityhas component activityw 'has process component' p if p and w are processes, w 'has part' p and w is such that it can be directly disassembled into into n parts p, p2, p3, ..., pn, where these parts are of similar type.has component processA relationship that holds between between a receptor and an chemical entity, typically a small molecule or peptide, that carries information between cells or compartments of a cell and which binds the receptor and regulates its effector function.has liganddirectly regulated byProcess(P2) is directly negatively regulated by process(P1) iff: P1 negatively regulates P2 via direct physical interaction between an agent executing P1 (or some part of P1) and an agent executing P2 (or some part of P2). For example, if protein A has protein binding activity(P1) that targets protein B and this binding negatively regulates the kinase activity (P2) of protein B then P2 directly negatively regulated by P1.directly negatively regulated byProcess(P2) is directly negatively regulated by process(P1) iff: P1 negatively regulates P2 via direct physical interaction between an agent executing P1 (or some part of P1) and an agent executing P2 (or some part of P2). For example, if protein A has protein binding activity(P1) that targets protein B and this binding negatively regulates the kinase activity (P2) of protein B then P2 directly negatively regulated by P1.GOC:dosProcess(P2) is directly postively regulated by process(P1) iff: P1 positively regulates P2 via direct physical interaction between an agent executing P1 (or some part of P1) and an agent executing P2 (or some part of P2). For example, if protein A has protein binding activity(P1) that targets protein B and this binding positively regulates the kinase activity (P2) of protein B then P2 is directly postively regulated by P1.directly positively regulated byProcess(P2) is directly postively regulated by process(P1) iff: P1 positively regulates P2 via direct physical interaction between an agent executing P1 (or some part of P1) and an agent executing P2 (or some part of P2). For example, if protein A has protein binding activity(P1) that targets protein B and this binding positively regulates the kinase activity (P2) of protein B then P2 is directly postively regulated by P1.GOC:dosA 'has effector activity' B if A and B are GO molecular functions (GO_0003674), A 'has component activity' B and B is the effector (output function) of B. Each compound function has only one effector activity.has effector activityA 'has effector activity' B if A and B are GO molecular functions (GO_0003674), A 'has component activity' B and B is the effector (output function) of B. Each compound function has only one effector activity.GOC:dosbefore or simultaneous withRelation between occurrents, shares start and end boundaries.RO:0002082coincides_withis_equal_touberonsimultaneous_withsimultaneous withsimultaneous_withRelation between occurrents, shares start and end boundaries.Allen:is_equal_toends afterX immediately_preceded_by Y iff: end(X) simultaneous_with start(Y)A non-transitive temporal relation in which one process immediately precedes another process, such that there is no interval of time between the two processes[SIO:000251].RO:0002087directly preceded byis directly preceded byis immediately preceded bystarts_at_end_ofDananassae_stages_ontologyDmojavensis_stages_ontologyDpseudobscura_stages_ontologyDsimulans_stages_ontologyDvirilis_stages_ontologyDyakuba_stages_ontologyFlyBase development CVbonobo_stages_ontologycat_stages_ontologycavy_stages_ontologychicken_stages_ontologychimpanzee_stages_ontologycow_stages_ontologydog_stages_ontologygorilla_stages_ontologyhedgehog_stages_ontologyhorse_stages_ontologyhuman_stages_ontologylizard_stages_ontologymedaka_ontologymouse_stages_ontologyopossum_stages_ontologyorangutan_stages_ontologypig_stages_ontologyplatypus_stages_ontologypufferfish_stages_ontologyrabbit_stages_ontologyrat_stages_ontologyrhesus_macaque_stages_ontologyuberonimmediately_preceded_bySame as starts_at_end_ofimmediately preceded byimmediately_preceded_byA non-transitive temporal relation in which one process immediately precedes another process, such that there is no interval of time between the two processes[SIO:000251].SIO:000251is immediately preceded bySIO:000251RO:0002090FlyBase development CVends_at_start_ofends_at_start_ofimmediately precedesA overlaps B if they share some part in common.BFO_0000051 some (BFO_0000050 some ?Y)RO:0002131uberonoverlapsoverlapsRelation between a 'neuron projection bundle' and a region in which one or more of its component neuron projections either synapses to targets or receives synaptic input.
T innervates some R
Expands_to: T has_fasciculating_neuron_projection that synapse_in some R.RO:0002134uberoninnervateshttp://code.google.com/p/obo-relations/issues/detail?id=6innervatesinnervatesX continuous_with Y if and only if X and Y share a fiat boundary.RO:0002150uberoncontinuous_withcontinuous withcontinuous_withRO:0002158uberonhomologous_tohomologous_toRO:0002159uberonserially_homologous_toserially homologous toserially_homologous_toS only_in_taxon T iff: S SubClassOf in_taxon only Tx only in taxon y if and only if x is in taxon y, and there is no other organism z such that y!=z a and x is in taxon z.RO:0002160rhesus_macaque_stages_ontologyuberononly_in_taxononly in taxononly_in_taxonS only_in_taxon T iff: S SubClassOf in_taxon only Tx is in taxon y if an only if y is an organism, and the relationship between x and y is one of: part of (reflexive), developmentally preceded by, derives from, secreted by, expressed.RO:0002162uberonin_taxonin taxonBinary relationship: x connected_to y if and only if there exists some z such that z connects x and y in a ternary connected_to(x,y,z) relationship.a is connected to b if and only if a and b are discrete structure, and there exists some connecting structure c, such that c connects a and bRO:0002170uberonconnected_toConnection does not imply overlaps.connected toconnected toBinary relationship: x connected_to y if and only if there exists some z such that z connects x and y in a ternary connected_to(x,y,z) relationship.Binary relationship: z connects x if and only if there exists some y such that z connects x and y in a ternary connected_to(x,y,z) relationship.c connects a if and only if there exist some b such that a and b are similar parts of the same system, and c connects b, specifically, c connects a with b. When one structure connects two others it unites some aspect of the function or role they play within the system.this is currently used for both structural relationships (such as between a valve and the chamber it connects) and abstract relationships (anatomical lines and the entities they connect)RO:0002176uberonconnectsconnectsconnectsBinary relationship: z connects x if and only if there exists some y such that z connects x and y in a ternary connected_to(x,y,z) relationship.a is attached to part of b if a is attached to b, or a is attached to some p, where p is part of b.RO:0002177uberonattaches_to_part_ofattached to part ofattaches_to_part_oftruetrueRelation between an arterial structure and another structure, where the arterial structure acts as a conduit channeling fluid, substance or energy.relation between an artery and the structure is supplies with blood.RO:0002178arterial supply ofuberonsuppliessource: FMAsuppliessuppliesarterial supply ofFMA:86003Relation between an collecting structure and another structure, where the collecting structure acts as a conduit channeling fluid, substance or energy away from the other structure.RO:0002179drains blood fromdrains fromuberondrainssource: Wikipediadrainsdrainsw 'has component' p if w 'has part' p and w is such that it can be directly disassembled into into n parts p, p2, p3, ..., pn, where these parts are of similar type.RO:0002180uberonhas_componenthas componenthas componentx develops from y if and only if either (a) x directly develops from y or (b) there exists some z such that x directly develops from z and z develops from yRO:0002202uberondevelops_fromdevelops fromdevelops_frominverse of develops fromRO:0002203uberondevelops_intodevelops intodevelops_intoCandidate definition: x directly_develops from y if and only if there exists some developmental process (GO:0032502) p such that x and y both participates in p, and x is the output of p and y is the input of p, and a substantial portion of the matter of y comes from x, and the start of x is coincident with or after the end of yRO:0002207uberondirectly_develops_fromdirectly develops fromdirectly_develops_frominverse of directly develops fromdirectly develops intoprocess(P1) regulates process(P2) iff: P1 results in the initiation or termination of P2 OR affects the frequency of its initiation or termination OR affects the magnitude or rate of output of P2.RO:0002211regulatesregulatesregulatesProcess(P1) negatively regulates process(P2) iff: P1 terminates P2, or P1 descreases the the frequency of initiation of P2 or the magnitude or rate of output of P2.RO:0002212negatively_regulatesnegatively regulatesnegatively regulatesProcess(P1) postively regulates process(P2) iff: P1 initiates P2, or P1 increases the the frequency of initiation of P2 or the magnitude or rate of output of P2.RO:0002213positively_regulatespositively regulatespositively regulatesA relation between a material entity (such as a cell) and a process, in which the material entity has the ability to carry out the process. RO:0002215uberoncapable_ofcapable ofcapable ofc stands in this relationship to p if and only if there exists some p' such that c is capable_of p', and p' is part_of p.RO:0002216uberoncapable_of_part_ofcapable of part ofcapable of part oftruex actively participates in y if and only if x participates in y and x realizes some active roleactively participates inx has participant y if and only if x realizes some active role that inheres in yhas active participantx surrounded_by y if and only if (1) x is adjacent to y and for every region r that is adjacent to x, r overlaps y (2) the shared boundary between x and y occupies the majority of the outermost boundary of xx surrounded_by y iff: x is adjacent to y and for every region r adjacent to x, r overlaps yRO:0002219uberonsurrounded_bysurrounded bysurrounded_byx surrounded_by y iff: x is adjacent to y and for every region r adjacent to x, r overlaps yx adjacent to y if and only if x and y share a boundary.x adjacent_to y iff: x and y share a boundaryRO:0002220uberonadjacent_toadjacent toadjacent_toinverse of surrounded byinverse of surrounded_byRO:0002221uberonsurroundssurroundssurroundsinverse of surrounded_bytemporally related toRelation between occurrents, shares a start boundary with.inverse of starts withRO:0002223uberonstartsstartsstartsRelation between occurrents, shares a start boundary with.Allen:startsx starts with y if and only if x has part y and the time point at which x starts is equivalent to the time point at which y starts. Formally: α(y) = α(x) ∧ ω(y) < ω(x), where α is a function that maps a process to a start point, and ω is a function that maps a process to an end point.RO:0002224uberonstarts_withstarts withstarts withx develops from part of y if and only if there exists some z such that x develops from z and z is part of yRO:0002225uberondevelops_from_part_ofdevelops from part ofdevelops_from_part_ofx develops_in y if x is located in y whilst x is developingRO:0002226uberondevelops_inThis relation take from EHDAA2 - precise semantics yet to be defineddevelops indevelops_inRelation between occurrents, shares an end boundary with.inverse of ends withRO:0002229finishesuberonendsendsendsRelation between occurrents, shares an end boundary with.Allen:startsZFS:finishesx ends with y if and only if x has part y and the time point at which x ends is equivalent to the time point at which y ends. Formally: α(y) > α(x) ∧ ω(y) = ω(x), where α is a function that maps a process to a start point, and ω is a function that maps a process to an end point.RO:0002230uberonends_withends withends withx 'has starts location' y if and only if there exists some process z such that x 'starts with' z and z 'occurs in' yhas start locationx 'has end location' y if and only if there exists some process z such that x 'ends with' z and z 'occurs in' yhas end locationp has input c iff: p is a process, c is a material entity, c is a participant in p, c is present at the start of p, and the state of c is modified during p.has inputp has output c iff c is a participant in p, c is present at the end of p, and c is not present at the beginning of p.has outputx has developmental contribution from y iff x has some part z such that z develops from yRO:0002254uberonhas_developmental_contribution_fromhas developmental contribution fromhas developmental contribution frominverse of has developmental contribution fromRO:0002255uberondevelopmentally_contributes_todevelopmentally contributes todevelopmentally_contributes_tot1 developmentally_induced_by t2 if there is a process of organ induction (GO:0001759) with t1 and t2 as interacting participants. t2 causes t1 to change its fate from a precursor tissue type T to T', where T' develops_from T.t1 induced_by t2 if there is a process of developmental induction (GO:0031128) with t1 and t2 as interacting participants. t2 causes t1 to change its fate from a precursor anatomical structure type T to T', where T' develops_from TRO:0002256uberondevelopmentally_induced_bysources for developmentally_induced_by relationships in Uberon: Developmental Biology, Gilbert, 8th edition, figure 6.5(F)developmentally induced bydevelopmentally_induced_byt1 developmentally_induced_by t2 if there is a process of organ induction (GO:0001759) with t1 and t2 as interacting participants. t2 causes t1 to change its fate from a precursor tissue type T to T', where T' develops_from T.GO:0001759Inverse of developmentally induced bydevelopmentally inducesCandidate definition: x developmentally related to y if and only if there exists some developmental process (GO:0032502) p such that x and y both participates in p, and x is the output of p and y is the input of pRO:0002258uberondevelopmentally_preceded_bydevelopmentally preceded bydevelopmentally preceded byc acts upstream of p if and only if c enables some f that is involved in p' and p' occurs chronologically before p, is not part of p, and affects the execution of p. c is a material entity and f, p, p' are processes.acts upstream ofc acts upstream of or within p if c is enables f, and f is causally upstream of or within p. c is a material entity and p is an process.acts upstream of or withinx developmentally replaces y if and only if there is some developmental process that causes x to move or to cease to exist, and for the site that was occupied by x to become occupied by y, where y either comes into existence in this site or moves to this site from somewhere elseRO:0002285uberondevelopmentally_replacesdevelopmentally replacesdevelopmentally_replacesInverse of developmentally preceded bydevelopmentally succeeded bypart of developmental precursor ofcausally upstream of, positive effectcausally upstream of, negative effectRO:0002322adapted_foruberonconfers_advantage_inconfers advantage inconfers_advantage_inenablesA grouping relationship for any relationship directly involving a function, or that holds because of a function of one of the related entities.RO:0002328uberonfunctionally_related_tofunctionally related tofunctionally related tothis relation holds between c and p when c is part of some c', and c' is capable of p.RO:0002329uberonpart_of_structure_that_is_capable_ofpart of structure that is capable ofpart of structure that is capable oftruec involved_in p if and only if c enables some process p', and p' is part of pinvolved ininverse of enablesenabled byinverse of regulatesregulated byinverse of negatively regulatesnegatively regulated byinverse of positively regulatespositively regulated byis member of is a mereological relation between a item and a collection.RO:0002350uberonmember_ofmember ofmember ofhas member is a mereological relation between a collection and an item.RO:0002351uberonhas_memberhas memberhas memberinverse of has inputRO:0002352uberoninput_ofinput ofinput ofinverse of has outputRO:0002353uberonoutput_ofoutput ofoutput ofa is attached to b if and only if a and b are discrete objects or object parts, and there are physical connections between a and b such that a force pulling a will move b, or a force pulling b will move aRO:0002371uberonattaches_toattached toattaches_tom has_muscle_origin s iff m is attached_to s, and it is the case that when m contracts, s does not move. The site of the origin tends to be more proximal and have greater mass than what the other end attaches to.m has_muscle_origin s iff m is attaches_to s, and it is the case that when m contracts, s does not move. The site of the origin tends to be more proximal and have greater mass than what the other end attaches to.RO:0002372uberonhas_muscle_originThe origin is the end of a muscle that attaches to the more fixed part of the skeleton, which is the proximal end in limb muscleshas muscle originhas_muscle_originWe need to import uberon muscle to create a stricter domain constraintm has_muscle_origin s iff m is attaches_to s, and it is the case that when m contracts, s does not move. The site of the origin tends to be more proximal and have greater mass than what the other end attaches to.m has_muscle_insertion s iff m is attaches_to s, and it is the case that when m contracts, s moves. Insertions are usually connections of muscle via tendon to bone.m has_muscle_insertion s iff m is attaches_to s, and it is the case that when m contracts, s moves. Insertions are usually connections of muscle via tendon to bone.RO:0002373uberonhas_muscle_insertionThe insertion is the point of attachment of a muscle that moves the most when the muscle shortens, or the most distal end of limb muscleshas muscle insertionhas_muscle_insertionWe need to import uberon muscle into RO to use as a stricter domain constraintm has_muscle_insertion s iff m is attaches_to s, and it is the case that when m contracts, s moves. Insertions are usually connections of muscle via tendon to bone.x has_fused_element y iff: there exists some z : x has_part z, z homologous_to y, and y is a distinct element, the boundary between x and z is largely fiatx has_fused_element y iff: there exists some z : x has_part z, z homologous_to y, and y is a distinct element, the boundary between x and z is largely fiatRO:0002374uberonhas_fused_elementA single bone in one species may correspond to the fusion of two or more bones found as distinct elements in another. For example, tibiofibula has_fused_element tibia. A has_fused_element B does not imply that A has_part some B, rather than A has_part some B', where B' is not a subtype of B (because B is a distinct element but B' is a regional part) but has some evolutionary relationship to B.derived from ancestral fusion ofhas_fused_elementA relationship that holds between two material entities in a system of connected structures, where the branching relationship holds based on properties of the connecting network.in branching relationship withx tributary_of y if and only if x a channel for the flow of a substance into y, where y is larger than x. If x and y are hydrographic features, then y is the main stem of a river, or a lake or bay, but not the sea or ocean. If x and y are anatomical, then y is a vein.RO:0002376uberondrains intotributary_oftributary oftributary_ofdrains intodbpowl:drainsTox is a branching part of y if and only if x is part of y and x is connected directly or indirectly to the main stem of ywe need to check if FMA branch_of implies part_of. the relation we intend to use here should - for example, see vestibulocochlear nerveRO:0002380uberonbranching_part_ofbranching part ofbranching_part_ofx has developmental potential involving y iff x is capable of a developmental process with output y. y may be the successor of x, or may be a different structure in the vicinity (as for example in the case of developmental induction).has developmental potential involvingx has potential to developmentrally contribute to y iff x developmentally contributes to y or x is capable of developmentally contributing to yx has potential to developmentrally contribute to y iff x developmentally contributes to y or x is capable of developmentally contributing to yRO:0002385uberonhas_potential_to_developmentally_contribute_tohas potential to developmentally contribute tohas potential to developmentally contribute tox has potential to developmentally induce y iff x developmentally induces y or x is capable of developmentally inducing yhas potential to developmentally inducex has the potential to develop into y iff x develops into y or if x is capable of developing into yx has the potential to develop into y iff x develops into y or if x is capable of developing into yRO:0002387uberonhas_potential_to_develop_intohas potential to develop intohas potential to develop intox has potential to directly develop into y iff x directly develops into y or x is capable of directly developing into yx has potential to directly develop into y iff x directly develops into y or x is capable of directly developing into yRO:0002388uberonhas_potential_to_directly_develop_intohas potential to directly develop intohas potential to directly develop intoinverse of upstream ofcausally downstream ofimmediately causally downstream ofp is causally upstream of q if and only if p precedes q and p and q are linked in a causal chaincausally upstream ofp is immediately causally upstream of q iff both (a) p immediately precedes q and (b) p is causally upstream of q. In addition, the output of p must be an input of q.immediately causally upstream ofp 'causally upstream or within' q iff (1) the end of p is before the end of q and (2) the execution of p exerts some causal influence over the outputs of q; i.e. if p was abolished or the outputs of p were to be modified, this would necessarily affect q.causally upstream of or withininverse of causally upstream of or withincausally downstream of or withinc involved in regulation of p if c is involved in some p' and p' regulates some pinvolved in regulation ofc involved in regulation of p if c is involved in some p' and p' positively regulates some pinvolved in positive regulation ofc involved in regulation of p if c is involved in some p' and p' negatively regulates some pinvolved in negative regulation ofc involved in or regulates p if and only if either (i) c is involved in p or (ii) c is involved in regulation of pinvolved in or involved in regulation ofc executes activity in d if and only if c enables p and p occurs_in d. Assuming no action at a distance by gene products, if a gene product enables (is capable of) a process that occurs in some structure, it must have at least some part in that structure.is active intruec executes activity in d if and only if c enables p and p occurs_in d. Assuming no action at a distance by gene products, if a gene product enables (is capable of) a process that occurs in some structure, it must have at least some part in that structure.GOC:cjmGOC:dosp contributes to morphology of w if and only if a change in the morphology of p entails a change in the morphology of w. Examples: every skull contributes to morphology of the head which it is a part of. Counter-example: nuclei do not generally contribute to the morphology of the cell they are part of, as they are buffered by cytoplasm.RO:0002433uberoncontributes_to_morphology_ofcontributes to morphology ofA relationship that holds between two entities in which the processes executed by the two entities are causally connected.interacts withAn interaction relationship in which the two partners are molecular entities that directly physically interact with each other for example via a stable binding interaction or a brief interaction during which one modifies the other.molecularly interacts withphosphorylatesHolds between molecular entities A and B where A can physically interact with B and in doing so regulates a process that B is capable of. For example, A and B may be gene products and binding of B by A regulates the kinase activity of B.activity directly regulates activity ofHolds between molecular entities A and B where A can physically interact with B and in doing so negatively regulates a process that B is capable of. For example, A and B may be gene products and binding of B by A negatively regulates the kinase activity of B.activity directly negatively regulates activity ofHolds between molecular entities A and B where A can physically interact with B and in doing so positively regulates a process that B is capable of. For example, A and B may be gene products and binding of B by A positively regulates the kinase activity of B.activity directly positively regulates activity ofx composed_primarily_of y if and only if more than half of the mass of x is made from y or units of the same type as y.x composed_primarily_of y iff: more than half of the mass of x is made from parts of yRO:0002473uberoncomposed_primarily_ofcomposed primarily ofRO:0002476uberonchild_nucleus_ofchild nucleus ofRO:0002477uberonchild_nucleus_of_in_hermaphroditechild nucleus of in hermaphroditeRO:0002478uberonchild_nucleus_of_in_malechild nucleus of in malep has part that occurs in c if and only if there exists some p1, such that p has_part p1, and p1 occurs in c.has part that occurs intruerelation between structure and stageRelation between continuant c and occurrent s, such that every instance of c comes into existing during some s.x existence starts during y if and only if the time point at which x starts is after or equivalent to the time point at which y starts and before or equivalent to the time point at which y ends. Formally: x existence starts during y iff α(x) >= α(y) & α(x) <= ω(y).RO:0002488begins_to_exist_duringuberonexistence_starts_duringexistence starts duringRelation between continuant c and occurrent s, such that every instance of c comes into existing during some s.Relation between continuant and occurrent, such that c comes into existence at the start of p.x starts ends with y if and only if the time point at which x starts is equivalent to the time point at which y starts. Formally: x existence starts with y iff α(x) = α(y).RO:0002489uberonexistence_starts_withexistence starts withRelation between continuant and occurrent, such that c comes into existence at the start of p.x existence overlaps y if and only if either (a) the start of x is part of y or (b) the end of x is part of y. Formally: x existence starts and ends during y iff (α(x) >= α(y) & α(x) <= ω(y)) OR (ω(x) <= ω(y) & ω(x) >= α(y))existence overlapsRelation between continuant c and occurrent s, such that every instance of c ceases to exist during some s, if it does not die prematurely.x existence ends during y if and only if the time point at which x ends is before or equivalent to the time point at which y ends and after or equivalent to the point at which y starts. Formally: x existence ends during y iff ω(x) <= ω(y) and ω(x) >= α(y).RO:0002492ceases_to_exist_duringuberonexistence_ends_duringexistence ends duringRelation between continuant c and occurrent s, such that every instance of c ceases to exist during some s, if it does not die prematurely.Relation between continuant and occurrent, such that c ceases to exist at the end of p.x existence ends with y if and only if the time point at which x ends is equivalent to the time point at which y ends. Formally: x existence ends with y iff ω(x) = ω(y).RO:0002493uberonexistence_ends_withexistence ends withRelation between continuant and occurrent, such that c ceases to exist at the end of p.x transformation of y if x is the immediate transformation of y, or is linked to y through a chain of transformation relationshipsRO:0002494transforms fromuberontransformation_oftransformation oftransforms fromSIO:000657x immediate transformation of y iff x immediately succeeds y temporally at a time boundary t, and all of the matter present in x at t is present in y at t, and all the matter in y at t is present in x at tRO:0002495direct_transformation_ofimmediately transforms fromuberonimmediate_transformation_ofimmediate transformation ofdirect_transformation_ofimmediately transforms fromSIO:000658x existence starts during or after y if and only if the time point at which x starts is after or equivalent to the time point at which y starts. Formally: x existence starts during or after y iff α (x) >= α (y).RO:0002496uberonexistence_starts_during_or_afterexistence starts during or afterx existence ends during or before y if and only if the time point at which x ends is before or equivalent to the time point at which y ends.RO:0002497uberonexistence_ends_during_or_beforeexistence ends during or beforeA relationship between a material entity and a process where the material entity has some causal role that influences the processcausal agent in processp is causally related to q if and only if p or any part of p and q or any part of q are linked by a chain of events where each event pair is one of direct activation or direct inhibition. p may be upstream, downstream, part of or a container of q.causal relation between processescausal relation between material entitiesA relation between a segment or subdivision of an organism and the maximal subdivision of material entities that provides structural support for that segment or subdivision.A relation between a subdivision of an organism and the single subdivision of skeleton that provides structural support for that subdivision.RO:0002551uberonhas sekeletal supporthas supporting frameworkhas_skeletonhas skeletonA relation between a subdivision of an organism and the single subdivision of skeleton that provides structural support for that subdivision.causally influenced byHolds between materal entities a and b if the activity of a is causally upstream of the activity of b, or causally upstream of a an activity that modifies bcausally influencesA relation that holds between elements of a musculoskeletal system or its analogs.biomechanically related tom1 has_muscle_antagonist m2 iff m1 acts in opposition to m2, and m2 is responsible for returning the structure to its initial position.m1 has_muscle_antagonist m2 iff m1 has_muscle_insertion s, m2 has_muscle_insection s, m1 acts in opposition to m2, and m2 is responsible for returning the structure to its initial position.RO:0002568uberonhas_muscle_antagonisthas muscle antagonisthas_muscle_antagonistm1 has_muscle_antagonist m2 iff m1 acts in opposition to m2, and m2 is responsible for returning the structure to its initial position.inverse of branching part ofRO:0002569uberonhas_branching_parthas branching partx lumen_of y iff x is the space or substance that is part of y and does not cross any of the inner membranes or boundaries of y that is maximal with respect to the volume of the convex hull.RO:0002571uberonlumen_oflumen ofs is luminal space of x iff s is lumen_of x and s is an immaterial entityRO:0002572uberonluminal_space_ofluminal space ofinverse of has skeletonRO:0002576uberonskeleton_ofskeleton ofProcess(P1) directly regulates process(P2) iff: P1 regulates P2 via direct physical interaction between an agent executing P1 (or some part of P1) and an agent executing P2 (or some part of P2). For example, if protein A has protein binding activity(P1) that targets protein B and this binding regulates the kinase activity (P2) of protein B then P1 directly regulates P2.directly regulatess 'has part structure that is capable of' p if and only if there exists some part x such that s 'has part' x and x 'capable of' phas part structure that is capable ofA relationship that holds between a material entity and a process in which causality is involved, with either the material entity or some part of the material entity exerting some influence over the process, or the process influencing some aspect of the material entity.causal relation between material entity and a processHolds between c and p if and only if c is capable of some activity a, and a regulates p.capable of regulatingHolds between c and p if and only if c is capable of some activity a, and a negatively regulates p.capable of negatively regulatingHolds between c and p if and only if c is capable of some activity a, and a positively regulates p.capable of positively regulatingInverse of 'causal agent in process'process has causal agentProcess(P1) directly postively regulates process(P2) iff: P1 positively regulates P2 via direct physical interaction between an agent executing P1 (or some part of P1) and an agent executing P2 (or some part of P2). For example, if protein A has protein binding activity(P1) that targets protein B and this binding positively regulates the kinase activity (P2) of protein B then P1 directly positively regulates P2.directly positively regulatesProcess(P1) directly negatively regulates process(P2) iff: P1 negatively regulates P2 via direct physical interaction between an agent executing P1 (or some part of P1) and an agent executing P2 (or some part of P2). For example, if protein A has protein binding activity(P1) that targets protein B and this binding negatively regulates the kinase activity (P2) of protein B then P1 directly negatively regulates P2.directly negatively regulatesa produces b if some process that occurs_in a has_output b, where a and b are material entities. Examples: hybridoma cell line produces monoclonal antibody reagent; chondroblast produces avascular GAG-rich matrix.RO:0003000uberonproducesproducesproducesa produced_by b iff some process that occurs_in b has_output a.RO:0003001uberonproduced_byproduced byproduced_byHolds between an entity and an process P where the entity enables some larger compound process, and that larger process has-part P.enables subfunctionacts upstream of or within, positive effectacts upstream of or within, negative effectc 'acts upstream of, positive effect' p if c is enables f, and f is causally upstream of p, and the direction of f is positiveacts upstream of, positive effectc 'acts upstream of, negative effect' p if c is enables f, and f is causally upstream of p, and the direction of f is negativeacts upstream of, negative effectcausally upstream of or within, negative effectcausally upstream of or within, positive effectUBPROP:0000004uberonprovenance_notesobsolete provenance_notestruetrueuberonanastomoses withx anteriorly_connected_to y iff the anterior part of x is connected to y. i.e. x connected_to y and x posterior_to y.uberonanteriorly connected tox anteriorly_connected_to y iff the anterior part of x is connected to y. i.e. x connected_to y and x posterior_to y.carriesuberonchannel foruberonchannels_fromuberonchannels_intox is a conduit for y iff y passes through the lumen of x.uberonconduit forx distally_connected_to y iff the distal part of x is connected to y. i.e. x connected_to y and x proximal_to y.uberondistally connected tox distally_connected_to y iff the distal part of x is connected to y. i.e. x connected_to y and x proximal_to y.uberonexistence starts and ends duringuberonextends_fibers_intoRelationship between a fluid and a material entity, where the fluid is the output of a realization of a filtration role that inheres in the material entity.uberonRelationship between a fluid and a filtration barrier, where the portion of fluid arises as a transformation of another portion of fluid on the other side of the barrier, with larger particles removedfiltered throughuberonhas_startX in_central_side Y <=> if Y is subdivided into left and right portions around some median divisor, all parts of X are closer to the median divisor than the outermost lateral sides.uberonin_central_side_ofhttps://github.com/obophenotype/uberon/wiki/Modeling-paired-structures-Design-PatternX in_central_side Y <=> if Y is subdivided into left and right portions around some median divisor, all parts of X are closer to the median divisor than the outermost lateral sides.BSPO:cjmuberonin_innermost_side_ofuberonin_outermost_side_ofa indirectly_supplies s iff a has a branch and the branch supplies or indirectly supplies sadd to ROuberonindirectly_suppliesuberonlayer part ofx posteriorly_connected_to y iff the posterior part of x is connected to y. i.e. x connected_to y and x anterior_to y.uberonposteriorly connected tox posteriorly_connected_to y iff the posterior part of x is connected to y. i.e. x connected_to y and x anterior_to y.uberonprotectsx proximally_connected_to y iff the proximal part of x is connected to y. i.e. x connected_to y and x distal_to y.uberonproximally connected tox proximally_connected_to y iff the proximal part of x is connected to y. i.e. x connected_to y and x distal_to y.uberonsexually_homologous_toc site_of p if c is the bearer of a disposition that is realized by a process that has p as partuberoncapable_of_has_partsite_ofuberonplaceholder relation. X = 'subdivision of A' and subdivision_of some B means that X is the mereological sum of A and Bsubdivision ofRelation between an anatomical structure (including cells) and a neuron that chemically synapses to it.uberonsynapsed by.uberontransitively anteriorly connected to.uberontransitively_connected to.uberontransitively distally connected to..uberontransitively proximally connected to.uberontrunk_part_oftruetruetruetruetruetruetruetruetruetruetruetruetruetruetruetruetrueAnatomical structure composed of a single cell.single-cell tissueAnatomical structure composed of a single cell.CARO:MAHThe inner space within a tube.tube lumenlumen of tubeThe inner space within a tube.AEO:JBA small cavity bounded by an epithelium.cavity of vesiclelumen of epithelial sacA small cavity bounded by an epithelium.AEO:JBA hole in a tissue.foramenA hole in a tissue.AEO:JBA tissue whose predominant feature is extracellular matrix which may or may not be highly hydrated or calcified.matrix-based tissueA tissue whose predominant feature is extracellular matrix which may or may not be highly hydrated or calcified.AEO:JBOssified structure that is predominantly extracellular matrix and forms part of the support system of the body.boneOssified structure that is predominantly extracellular matrix and forms part of the support system of the body.AEO:JBBone that is preformed in cartilage.endochondral boneBone that is preformed in cartilage.AEO:JBVAO:0000145Bone that forms directly from mesenchyme.membrane boneBone that forms directly from mesenchyme.AEO:JBVAO:0000023An endochondral bone that forms within tendenous or ligamentous matrix.sesamoid boneAn endochondral bone that forms within tendenous or ligamentous matrix.AEO:JBVAO:0000137Dense connective tissue made primarily of type II collagen.cartilageDense connective tissue made primarily of type II collagen.AEO:JBVAO:0000040A strap of predominantly extracellular matrix connecting two bones.ligamentA strap of predominantly extracellular matrix connecting two bones.AEO:JBA strap of predominantly extracellular matrix connecting a muscle to a bone.tendonA strap of predominantly extracellular matrix connecting a muscle to a bone.AEO:JBA sheet of extracellular matrix.aponeurosisA sheet of extracellular matrix.AEO:JBAn anatomical group whose component structures share a common function.non-connected functional systemAn anatomical group whose component structures share a common function.AEO:JBMulticellular anatomical structure with largely bona fide boundary that transduces some sensory stimulus to the nervous system.sense organMulticellular anatomical structure with largely bona fide boundary that transduces some sensory stimulus to the nervous system.AEO:JBFluid anatomical entity containing cells.fluid-based anatomical entityFluid anatomical entity containing cells.AEO:JBA multi-tissue structure that produces a secretion for use elsewhere in the body.glandA multi-tissue structure that produces a secretion for use elsewhere in the body.AEO:JBA gland that releases its secretion through a duct.exocrine gland.ducted glandA gland that releases its secretion through a duct.AEO:JBA gland that releases its secretion directly into the bloodstream, or equivalent for an invertebrate.endocrine gland.ductless glandA gland that releases its secretion directly into the bloodstream, or equivalent for an invertebrate.AEO:JBendocrine gland.AEO:JBAcellular anatomical structure whose predominant constituent is keratin.keratin-based structureAcellular anatomical structure whose predominant constituent is keratin.AEO:JBAcellular anatomical structure whose predominant constituent is chitin.chitin-based structureAcellular anatomical structure whose predominant constituent is chitin.AEO:JBThe region of the organism associated with the visceral organs.bodyThe region of the organism associated with the visceral organs.AEO:JBThe region of the body containing the brain and mouth.headThe region of the body containing the brain and mouth.AEO:JBThe region of the body connecting the head and the body.neckThe region of the body connecting the head and the body.AEO:JBAn external caudal extension of the body.tailAn external caudal extension of the body.AEO:JBEpithelium derived from mesenchyme.mesotheliumEpithelium derived from mesenchyme.AEO:JBAn epithelial structure capable of allowing fluid flow.epithelial tubeAn epithelial structure capable of allowing fluid flow.AEO:JBAn epithelial pouch with a single opening.epithelial sacAn epithelial pouch with a single opening.AEO:JBA group of connected epithelial tubes with a single portal.arborising epithelial duct systemA group of connected epithelial tubes with a single portal.AEO:JBA network of interlinking epithelial tubes.epithelial plexusA network of interlinking epithelial tubes.AEO:JBepithelial vesicleA closed epithelium with a lumen.epithelial vesicletrueA closed epithelium with a lumen.AEO:JBA tissue composed of myoblasts or muscle cells.muscle tissueA tissue composed of myoblasts or muscle cells.AEO:JBTissue composed predominantly of neurons.neural tissueTissue composed predominantly of neurons.AEO:JBA structure whose morphology or state of differentiation will change during normal development.developing anatomical structureA structure whose morphology or state of differentiation will change during normal development.AEO:JBA post-embryonic juvenile form which will undergo metamorphosis to become the adult.larvaA post-embryonic juvenile form which will undergo metamorphosis to become the adult.AEO:JBAn embryonic anatomical structure undergoing apoptosis.apoptosing developing anatomical entityAn embryonic anatomical structure undergoing apoptosis.AEO:JBAn embryonic entity that displays a physiological function but whose strucuture is not yet fully formed.functioning and developing structureAn embryonic entity that displays a physiological function but whose strucuture is not yet fully formed.AEO:JBEmbronic structure that contains stem cellsr that may contribute to its future development or maintenance or to its future development or maintenance of another tissue.developing structure with stem cellsEmbronic structure that contains stem cellsr that may contribute to its future development or maintenance or to its future development or maintenance of another tissue.AEO:JBAn embryonic anatomical entity that will turn into one or more other anatomical entities, perhaps with other anatomical entities, later in development.transitional anatomical structureAn embryonic anatomical entity that will turn into one or more other anatomical entities, perhaps with other anatomical entities, later in development.AEO:JBA group of neurons, usually outside the CNS, which relay neuronal signals.ganglionA group of neurons, usually outside the CNS, which relay neuronal signals.AEO:JBA localised domain of predominantly neuronal tissue in the central nervous system.neuronal nucleusA localised domain of predominantly neuronal tissue in the central nervous system.AEO:JBA group of neurons that provides a nervous supply.nerveA group of neurons that provides a nervous supply.AEO:JBA complex of interconnecting nerves.nerve plexusA complex of interconnecting nerves.AEO:JBA fasciculated bundle of neuron projections, largely or completely lacking synapses.neuron projection bundlenerve fiber tractA fasciculated bundle of neuron projections, largely or completely lacking synapses.CARO:0001001GO:0043005neuron projection bundleGO:0043005A tissue composed of striated muscle cells.striated muscle tissueA tissue composed of striated muscle cells.AEO:JBA tissue composed of smooth muscle cells.smooth muscle tissueA tissue composed of smooth muscle cells.AEO:JBA tissue composed of cardiac muscle cells.cardiac muscle tissueA tissue composed of cardiac muscle cells.AEO:JBA ring of smooth muscle cells whose contraction closes the opening of the ring.smooth muscle sphincterA ring of smooth muscle cells whose contraction closes the opening of the ring.AEO:JBA ring of striated muscle cells whose contraction closes the opening of the ring.striated muscle sphincterA ring of striated muscle cells whose contraction closes the opening of the ring.AEO:JBA group of not-yet-terminally-differentiatied cells that can pack in three dimensions.mesenchymal tissueA group of not-yet-terminally-differentiatied cells that can pack in three dimensions.AEO:JBMesenchyme with little extracellular matrix.dense mesenchyme tissueMesenchyme with little extracellular matrix.AEO:JBCell condensation that is an aggregation of mesenchymal cells that are committed to differentiate into chondroblasts and chondrocytes.cartilagenous condensationCell condensation that is an aggregation of mesenchymal cells that are committed to differentiate into chondroblasts and chondrocytes.AEO:JBGO:curatorVAO:0000092A delimited region of dense mesenchyme within looser mesenchyme.developing mesenchymal condensationA delimited region of dense mesenchyme within looser mesenchyme.AEO:JBA delimited region of dense mesenchyme within looser mesenchyme whose cells are committed to become myoblasts.pre-muscle condensationA delimited region of dense mesenchyme within looser mesenchyme whose cells are committed to become myoblasts.AEO:JBA delimited region of dense mesenchyme within looser mesenchyme whose cells are committed to become chondroblasts.pre-cartilage condensationA delimited region of dense mesenchyme within looser mesenchyme whose cells are committed to become chondroblasts.AEO:JBMesenchyme whose cells are embedded in obvious amounts fo extracellular matrix.loose mesenchyme tissueMesenchyme whose cells are embedded in obvious amounts fo extracellular matrix.AEO:JBMesenchymal cells that are migrating.migrating mesenchyme populationMesenchymal cells that are migrating.AEO:JBMulti-tissue mesenchymal structure one of whose parts contains stem cells that can replace other parts.mesenchymal tissue with stem cellsMulti-tissue mesenchymal structure one of whose parts contains stem cells that can replace other parts.AEO:JBThe collection of structures that form the exxtenal covering of the organism.organism surfacefThe collection of structures that form the exxtenal covering of the organism.AEO:JBThe exposed surface of a furrow or an incomplete tube.grooveThe exposed surface of a furrow or an incomplete tube.AEO:JBA raised strip of tissue.ridgeA raised strip of tissue.AEO:JBThe rigid support system for the body.skeletal systemThe rigid support system for the body.AEO:JBVAO:0000027That part of the conceptus that will form the organism.embryoThat part of the conceptus that will form the organism.AEO:JBAnlagen are populations of contiguous cells, typically arranged in one plane, that are morphologically indistinct, but that already correspond in extent to a later organ/tissue.anlageAnlagen are populations of contiguous cells, typically arranged in one plane, that are morphologically indistinct, but that already correspond in extent to a later organ/tissue.AEO:JBPrimordia are populations of contiguous cells that are morphologically distinct and already correspond in extent to a later organ/tissue.primordiumPrimordia are populations of contiguous cells that are morphologically distinct and already correspond in extent to a later organ/tissue.AEO:JBAppendage of an animal used for locomotion or grasping.limbAppendage of an animal used for locomotion or grasping.AEO:JBMulticellular anatomical structure with largely bona fide boundary that extends outwards from or is part of the organism surface and transduces some sensory stimulus to the nervous system.surface sense organMulticellular anatomical structure with largely bona fide boundary that extends outwards from or is part of the organism surface and transduces some sensory stimulus to the nervous system.AEO:JBA part of the body present only in a specific gender.gender-specific anatomical structureA part of the body present only in a specific gender.AEO:JBA part of the body present only in males.male anatomical structureA part of the body present only in males.AEO:JBA part of the body present only in females.female anatomical structureA part of the body present only in females.AEO:JBA part of the body present only in hermaphrodites.hermaphrodite anatomical structureA part of the body present only in hermaphrodites.AEO:JBA flexible joint between two bones that is made of unossified connective tissue.fibrous jointA flexible joint between two bones that is made of unossified connective tissue.AEO:JBThe articular cartilage covering of the region of bone within a synoval joint.joint-associated cartilageThe articular cartilage covering of the region of bone within a synoval joint.AEO:JBCartilage that may provide the template for an endochondral bone or that may be a disinct entity in the skeleton.non-joint-associated cartilageCartilage that may provide the template for an endochondral bone or that may be a disinct entity in the skeleton.AEO:JBThe epithelial membrane between bone ends that forms the lateral borders of the synovial cavity and secretes synovial fluid.synovial membraneThe epithelial membrane between bone ends that forms the lateral borders of the synovial cavity and secretes synovial fluid.AEO:JBA joint connecting two or more bones with cartilage at the bone ends and a synovial membrane that secretes synovial fluid conecting the bones and sealing the synovial cavity.synovial jointA joint connecting two or more bones with cartilage at the bone ends and a synovial membrane that secretes synovial fluid conecting the bones and sealing the synovial cavity.AEO:JBA component of the exoskeleton.exoskeletal tissueA component of the exoskeleton.AEO:JBThe cavity within the body that contains the visceral organs.body cavityThe cavity within the body that contains the visceral organs.AEO:JBMulti-tissue structure one of whose parts contains stem cells that can replace other parts.multi-tissue structure with stem cellsMulti-tissue structure one of whose parts contains stem cells that can replace other parts.AEO:JBAn acellular fluid portion of organism substance that is produced by the organism for some non-waste purpose.acellular fluid anatomical entityAn acellular fluid portion of organism substance that is produced by the organism for some non-waste purpose.AEO:JBMulti-tissue epithelial structure one of whose parts contains stem cells that can replace other parts.epithelial tissue with stem cellsMulti-tissue epithelial structure one of whose parts contains stem cells that can replace other parts.AEO:JBNon-material anatomical entity of two dimensions, that is demarcated by anatomical lines or points on the external or internal surfaces of anatomical structures.anatomical surface.anatomical surface featuretrueNon-material anatomical entity of two dimensions, that is demarcated by anatomical lines or points on the external or internal surfaces of anatomical structures.CARO:MAHOrgan or organ part that is attached to the body of an organism. For example a limb[GO, modified]. An appendage is an external body part, or natural prolongation, that protrudes from an organism's body, such as a vertebrate's limbs.appendageOrgan or organ part that is attached to the body of an organism. For example a limb[GO, modified]. An appendage is an external body part, or natural prolongation, that protrudes from an organism's body, such as a vertebrate's limbs.CARO:MAHAll the products of the fertilized egg.conceptusAll the products of the fertilized egg.AEO:JBThe part of the conceptus that may be lost before birth or will be discarded at birth, or when the embryo becomes an independent organism.extraembryonic componentThe part of the conceptus that may be lost before birth or will be discarded at birth, or when the embryo becomes an independent organism.AEO:JBAn anatomical structure present in the larval form of an animal.larval anatomical structureAn anatomical structure present in the larval form of an animal.AEO:JBA head-associated surface sense organ.antennaA head-associated surface sense organ.CARO:MAHA membranous structure with more than one cell type, one or more of which secretes mucus, that lines body passages which communicate with the exterior.mucosamucous membraneA membranous structure with more than one cell type, one or more of which secretes mucus, that lines body passages which communicate with the exterior.AEO:JBAn anatomical structure that, as part of its normal physiology, undergoes regeneration. Examples include endometrium and antlers.regenerating anatomical structureAn anatomical structure that, as part of its normal physiology, undergoes regeneration. Examples include endometrium and antlers.AEO:JBA group of neurons that provides a nervous response from a tissue.afferent nerveA group of neurons that provides a nervous response from a tissue.AEO:JBA group of neurons that provides a nervous signal to a tissue.efferent nerveA group of neurons that provides a nervous signal to a tissue.AEO:JBAn anatomical entity consisting of a single or a few multinucleated structures.syncytiumAn anatomical entity consisting of a single or a few multinucleated structures.AEO.:JBAn roughly circular indentation in a surface.pitAn roughly circular indentation in a surface.AEO:JBA roughly circular bulge in a surface.protuberanceA roughly circular bulge in a surface.AEO:JBAn epithelium that extends its surface area by peripheral movement.migrating epitheliumAn epithelium that extends its surface area by peripheral movement.AEO:JBAn epithelial tube that transports blood.blood vesselAn epithelial tube that transports blood.AEO:JBAn epithelial tube that transports blood away from the heart.arteryAn epithelial tube that transports blood away from the heart.AEO:JBAn epithelial tube that transports blood towards the heart.veinAn epithelial tube that transports blood towards the heart.AEO:JBAnatomical group whose component structures are arranged in a row.rowAnatomical group whose component structures are arranged in a row.DBft:DOSThe sum of all the anlagen and primordia that will develop into a single functional system.non-connected developing functional systemThe sum of all the anlagen and primordia that will develop into a single functional system.FBbt:DOSThe mesenchymal derivative of a somite that will migrate to surround the neural tube and form vertebrae.sclerotomeThe mesenchymal derivative of a somite that will migrate to surround the neural tube and form vertebrae.AEO:JBA delimited region of osteoblasts representing the early stages of bone formation.bone condensationA delimited region of osteoblasts representing the early stages of bone formation.AEO:JBThe bilaminar epithelium formed from the myotome and dermatome.dermomyotomeThe bilaminar epithelium formed from the myotome and dermatome.AEO:JBA volume that is mainly bounded but has an opening to another cavity or to the outside.open cavityA volume that is mainly bounded but has an opening to another cavity or to the outside.JB:AEOA cord of epithelial cells without a lumen and usually several cells thick.epithelial cordA cord of epithelial cells without a lumen and usually several cells thick.JB:AEOA simple coherent tissue or a localized population of similar cells that are actively migrating.migrating developing tissueA simple coherent tissue or a localized population of similar cells that are actively migrating.JB:AEOA domain of columnar epithelium in an embryo that represents the early stage of the development of the epithelial component of a new anatomical structure.developing epithelial placodeA domain of columnar epithelium in an embryo that represents the early stage of the development of the epithelial component of a new anatomical structure.JB:AEOA network of interlinked veins.vascular plexusA network of interlinked veins.JB:AEOEach of a set of hard, bony enamel-coated structures in the jaws of most vertebrates, used for biting and chewing.toothEach of a set of hard, bony enamel-coated structures in the jaws of most vertebrates, used for biting and chewing.JB:AEOAn anatomical space with at least one opening to another space or the exterior.open anatomical spaceAn anatomical space with at least one opening to another space or the exterior.JB:AEOAn anatomical space with no opening to another space or to the exterior.enclosed anatomical spaceAn anatomical space with no opening to another space or to the exterior.JB:AEOTissue that is predominantly made of fat cells.fat tissueTissue that is predominantly made of fat cells.AEO:JBA ganglion containing sensory neurons.sensory ganglionA ganglion containing sensory neurons.JB:AEOA ganglion that is part of the autonomic nervous system.autonomic ganglionA ganglion that is part of the autonomic nervous system.JB:AEOA localized group of blood capillaries.capillary bedA localized group of blood capillaries.JB:AEOAn acellular structure typically composed of collagen, glycoproteins and glycosaminoglycans.acellular extracellular matrixAn acellular structure typically composed of collagen, glycoproteins and glycosaminoglycans.JB:AEOA flattened appendage on a marine animal.finA flattened appendage on a marine animal.JB:AEOVAO:0000099A non-cellular substance released by a cell, gland or tissue.secretionA non-cellular substance released by a cell, gland or tissue.JB:AEOExcreta are bodily fluids consisting of waste matter, such as sweat or feces, discharged from the body.excretaExcreta are bodily fluids consisting of waste matter, such as sweat or feces, discharged from the body.JB:AEOAn epithelium within an embryo or larva that is undergoing a major developmental change.developing epitheliumAn epithelium within an embryo or larva that is undergoing a major developmental change.AEO:JBAn embryonic or larval epithelium that is committed to form part of the nervous system.neuroepitheliumAn embryonic or larval epithelium that is committed to form part of the nervous system.AEO:JBAn epithelium that is undergoing proliferation to provide large numbers of neuronal cells.proliferating neuroepitheliumAn epithelium that is undergoing proliferation to provide large numbers of neuronal cells.AEO:JBA neuroepithelium some of whose cells are undergoing terminal differentiation to become neuronal cells.differentiating neuroepitheliumA neuroepithelium some of whose cells are undergoing terminal differentiation to become neuronal cells.AEO:JBNeuronal tissue composed predominantly of axons.neuronal white matterNeuronal tissue composed predominantly of axons.AEO:JBA neuronal tissue composed predominantly of nerve bodies and neuronal support cells.neuronal grey matterA neuronal tissue composed predominantly of nerve bodies and neuronal support cells.AEO:JBAn extended columnar domain of predominantly neuronal tissue in the central nervous system.neuronal columnAn extended columnar domain of predominantly neuronal tissue in the central nervous system.AEO:JBA compact group of cells differentiating to become a ganglion or a neuronal nucleus.differentiating neuronal condensationA compact group of cells differentiating to become a ganglion or a neuronal nucleus.AEO:JBAn epithelial ball that forms from paraxial mesoderm.somiteAn epithelial ball that forms from paraxial mesoderm.JB:AEOA mesenchyme-derived anatomical entity undergoing a transtion to become another structure.developing mesenchymal structureA mesenchyme-derived anatomical entity undergoing a transtion to become another structure.AEO:JBA transitional population of migrating mesenchymal cells that derive from somites and that will become dermal cells.dermatomeA transitional population of migrating mesenchymal cells that derive from somites and that will become dermal cells.AEO:JBA transitional population of migrating mesenchymal cells that derive from somites and that will become muscle cells.myotomeA transitional population of migrating mesenchymal cells that derive from somites and that will become muscle cells.AEO:JBA germ cell population that has not undergone meiosis.developing germ cell populationA germ cell population that has not undergone meiosis.AEO:JBA population of cells that are predominantly immature or mature germ cells.reproductive cell populationA population of cells that are predominantly immature or mature germ cells.AEO:JBA group of cells capable of regenerating themselves and also of producing one or more populations of differentiated cells.stem cell populationA group of cells capable of regenerating themselves and also of producing one or more populations of differentiated cells.AEO:JBLizard developmental stage that refers to a lizard who is over 24 months old.aged stage (anolis)24.0lizard_developmental_stageGreen anoles can live up to seven years in captivity (see http://genomics.senescence.info/species/entry.php?species=Anolis_carolinensis). We arbitraly consider over 2 years as the starting point for aged stage. This is to improve as far as information is available.aged stage (anolis)Lizard developmental stage that refers to a lizard who is over 24 months old.Bgee:curatorAn entity that exists in full at any time in which it exists at all, persists through time while maintaining its identity and has no temporal parts.continuantAn entity that has temporal parts and that happens, unfolds or develops through time.An entity that has temporal parts and that happens, unfolds or develops through time. Sometimes also called perdurants.FlyBase development CVoccurrentoccurrentAn entity that has temporal parts and that happens, unfolds or develops through time. Sometimes also called perdurants.BFOC:ANONA continuant that is a bearer of quality and realizable entity entities, in which other entities inhere and which itself cannot inhere in anything.independent continuantAn occurrent that has temporal proper parts and for some time t, p s-depends_on some material entity at t.processqualityA continuant that inheres in or is borne by other entities. Every instance of A requires some specific instance of B which must always be the same.specifically dependent continuantobjectAn independent continuant that is spatially extended whose identity is independent of that of other entities and can be maintained through time.material entitymaterial entitytrueMature stage that refers to a cow who is over 12 years old, the usual upper limit for breeding age.aged stage (cow)12.0cow_developmental_stageCows have been known to live over 20 years.aged stage (cow)Mature stage that refers to a cow who is over 12 years old, the usual upper limit for breeding age.Bgee:curatoranatomical structurematerial anatomical entityMulti-cellular organism that has male and female sexes.monoecious organismgonochoristic organismMulti-cellular organism that has male and female sexes.CARO:MAHSequential hermaphroditic organism that produces gametes first of the male sex, and then later of the female sex.protandrous hermaphroditic organismSequential hermaphroditic organism that produces gametes first of the male sex, and then later of the female sex.CARO:MAHSequential hermaphroditic organism that produces gametes first of the female sex, and then later of the male sex.protogynous hermaphroditic organismSequential hermaphroditic organism that produces gametes first of the female sex, and then later of the male sex.CARO:MAHAnatomical space that is part of a cell.cell spaceAnatomical space that is part of a cell.CARO:mahMulti-cellular organism that does not produce gametes.asexual organismMulti-cellular organism that does not produce gametes.CARO:MAHCell that is an individual member of a species.single cell organismCell that is an individual member of a species.CARO:MAHA cell that is usually found in a two-dimensional sheet with a free surface. The cell has a cytoskeleton that allows for tight cell to cell contact and for cell polarity where apical part is directed towards the lumen and the basal part to the basal lamina.Epitheliocyteepithelial cellA cell that is usually found in a two-dimensional sheet with a free surface. The cell has a cytoskeleton that allows for tight cell to cell contact and for cell polarity where apical part is directed towards the lumen and the basal part to the basal lamina.FB:maGOC:tfmMESH:A.11.436eyelidcephalopod eyeThe glandular complex in cirrates that forms sperm packets and is a counterpart of the spermatophore-forming complex of other cephalopods. accessory gland complexThe glandular complex in cirrates that forms sperm packets and is a counterpart of the spermatophore-forming complex of other cephalopods. http://tolweb.org/accessory/Cephalopoda_Glossary?acc_id=587A sucker of the sepia or cuttlefish and related animals.acetabulumA sucker of the sepia or cuttlefish and related animals.http://tolweb.org/accessory/Cephalopoda_Glossary?acc_id=587A female that has mature eggs (these are frequently stored in the oviducts), or a male that has produced spermatophores (these are stored in Needham's sac).adult stageA female that has mature eggs (these are frequently stored in the oviducts), or a male that has produced spermatophores (these are stored in Needham's sac).http://tolweb.org/accessory/Cephalopoda_Glossary?acc_id=587A small flap on the lateral side of the anus.anal valveanal flapA small flap on the lateral side of the anus.http://tolweb.org/accessory/Cephalopoda_Glossary?acc_id=587Glands on or in the buccal mass that aid in preliminary digestion.anterior salivary glandGlands on or in the buccal mass that aid in preliminary digestion.http://tolweb.org/accessory/Cephalopod_Digestive_System?acc_id=1993Knob that projects inward from the posterior surface of the central depression in the funnel locking-apparatus of some squids.antitragusKnob that projects inward from the posterior surface of the central depression in the funnel locking-apparatus of some squids.http://tolweb.org/accessory/Cephalopoda_Glossary?acc_id=587Circular spots, generally light colored but often with complex pigmentation and of unknown function that occur in lines along the aboral surfaces of some arms and portions of the head in some opisthoteuthid cirrates.areolar spotCircular spots, generally light colored but often with complex pigmentation and of unknown function that occur in lines along the aboral surfaces of some arms and portions of the head in some opisthoteuthid cirrates.http://tolweb.org/accessory/Cephalopoda_Glossary?acc_id=587One of the circumoral appendages of cephalopods. In decapodiforms each member of the fourth pair of arms is modified to form a tentacle.circumoral armarmOne of the circumoral appendages of cephalopods. In decapodiforms each member of the fourth pair of arms is modified to form a tentacle.http://tolweb.org/accessory/Cephalopoda_Glossary?acc_id=587The relative sizes of arms arranged according to their length. The largest arm is indicated first and the shortest last. An example arm formula is IV>III=II>I. Here arm IV is the largest, followed by arm III which is the same size as arm II and both are larger than arm I.arm formulaThe relative sizes of arms arranged according to their length. The largest arm is indicated first and the shortest last. An example arm formula is IV>III=II>I. Here arm IV is the largest, followed by arm III which is the same size as arm II and both are larger than arm I.http://tolweb.org/accessory/Cephalopoda_Glossary?acc_id=587ventral armarm IVThe grappling structures on the oral surfaces the arms and tentacles, including both suckers and hooks. armature of the armsThe grappling structures on the oral surfaces the arms and tentacles, including both suckers and hooks. http://tolweb.org/accessory/Armature_of_Cephalopod_Arms?acc_id=2018Type of cusp arrangement on the rachadian tooth of the radula: multiple cusps seem to move laterally when viewing successive rachadian teeth from adjacent rows. a-seriationType of cusp arrangement on the rachadian tooth of the radula: multiple cusps seem to move laterally when viewing successive rachadian teeth from adjacent rows. http://tolweb.org/accessory/Cephalopoda_Glossary?acc_id=587Plane through an arm of an octopod that is predisposed to break when the arm is autotomized.autotomy planePlane through an arm of an octopod that is predisposed to break when the arm is autotomized.http://tolweb.org/accessory/Cephalopoda_Glossary?acc_id=587See cirrate shell terminology. basal shelfSee cirrate shell terminology. http://tolweb.org/accessory/Cephalopoda_Glossary?acc_id=587One of the two chitinous jaws of cephalopods. The dorsal beak is the &quot;upper&quot; beak and it inserts within the lower beak to tear tissue with a sissors-like cutting action.rostrumbeakOne of the two chitinous jaws of cephalopods. The dorsal beak is the &quot;upper&quot; beak and it inserts within the lower beak to tear tissue with a sissors-like cutting action.http://tolweb.org/accessory/Cephalopod_Beak_Terminology?acc_id=1980A ridge on the lower beak where the rostral edge merges onto the lateral wall. In most beaks the merger is smooth. This is a characteristic feature of the Onychoteuthidae.beak stepA ridge on the lower beak where the rostral edge merges onto the lateral wall. In most beaks the merger is smooth. This is a characteristic feature of the Onychoteuthidae.http://tolweb.org/accessory/Cephalopoda_Glossary?acc_id=587A large opening at the base of each gill lamella and between the primary afferent and efferent blood vessels of the gill. A branchial canal is absent in <strong>Nautilus</strong> , sepioid decapodiformes and cirrate octopods.branchial canalA large opening at the base of each gill lamella and between the primary afferent and efferent blood vessels of the gill. A branchial canal is absent in <strong>Nautilus</strong> , sepioid decapodiformes and cirrate octopods.http://tolweb.org/accessory/Cephalopoda_Glossary?acc_id=587The combination of arms and tentacles that surround the mouth.brachial crownThe combination of arms and tentacles that surround the mouth.http://tolweb.org/accessory/Cephalopod_Brachial_and_Buccal_Crowns?acc_id=1957The anterior-most part of the brain located ventral to the esophagus. The large axial nerve cords that run down the centers of the arms connect to this lobe. In octopods this lobe is fused with the rest of the subesophageal mass while in decapodiforms and <strong>Vampyroteuthis</strong> it is separate from the remaining brain.anterior subesophageal massanterior subesophageal mass of brainbrachial lobe of brainThe anterior-most part of the brain located ventral to the esophagus. The large axial nerve cords that run down the centers of the arms connect to this lobe. In octopods this lobe is fused with the rest of the subesophageal mass while in decapodiforms and <strong>Vampyroteuthis</strong> it is separate from the remaining brain.http://tolweb.org/accessory/Cephalopod_Brain_Terminology?acc_id=1944Elongate gland adjacent to and paralleling the gill where the gill attaches to the mantle wall.branchial glandElongate gland adjacent to and paralleling the gill where the gill attaches to the mantle wall.http://tolweb.org/accessory/Cephalopoda_Glossary?acc_id=587A pulsating gland at the base of the gill and through which the afferent blood to the gills flows. It contributes to the blood flow through the gill but also is the site of hemocyanin (the blood respiratory pigment) synthesis. branchial heartA pulsating gland at the base of the gill and through which the afferent blood to the gills flows. It contributes to the blood flow through the gill but also is the site of hemocyanin (the blood respiratory pigment) synthesis. http://tolweb.org/accessory/Cephalopoda_Glossary?acc_id=587Photophores located on the arms.brachial photophorePhotophores located on the arms.http://tolweb.org/accessory/Cephalopoda_Glossary?acc_id=587A very narrow and elongate anterior region of the head between the eyes and the base of the brachial crown. A branchial pillar is especially well developed in many young cranchiid squid.brachial pillarA very narrow and elongate anterior region of the head between the eyes and the base of the brachial crown. A branchial pillar is especially well developed in many young cranchiid squid.http://tolweb.org/accessory/Cephalopoda_Glossary?acc_id=587Medial portion of the central nervous system. It includes the subesophageal and supraesophageal masses but generally does not include the large optic lobes.cephalopod brainMedial portion of the central nervous system. It includes the subesophageal and supraesophageal masses but generally does not include the large optic lobes.http://tolweb.org/accessory/Cephalopod_Brain_Terminology?acc_id=1944Incubation of eggs by the parent. A characteristic feature of incirrate octopods but also found in some squid (e.g., Gonatidae).broodingIncubation of eggs by the parent. A characteristic feature of incirrate octopods but also found in some squid (e.g., Gonatidae).http://tolweb.org/accessory/Cephalopoda_Glossary?acc_id=587Muscular membrane that runs from the buccal support to the base of the adjacent arm. The position of the connective on the fourth arms was recognized in the early 20th century as an important character in interpreting phylogenetic relationships among decapodiforms.buccal connectiveMuscular membrane that runs from the buccal support to the base of the adjacent arm. The position of the connective on the fourth arms was recognized in the early 20th century as an important character in interpreting phylogenetic relationships among decapodiforms.http://tolweb.org/accessory/Cephalopod_Brachial_and_Buccal_Crowns?acc_id=1957Umbrella-like structure that surrounds the mouth and is surrounded by the brachial crown. It consists of buccal supports and the buccal membrane. The buccal crown is present in most decapodiforms but absent from all octopodiforms.buccal crownUmbrella-like structure that surrounds the mouth and is surrounded by the brachial crown. It consists of buccal supports and the buccal membrane. The buccal crown is present in most decapodiforms but absent from all octopodiforms.http://tolweb.org/accessory/Cephalopod_Brachial_and_Buccal_Crowns?acc_id=1957Muscular bulb at the beginning of the digestive system that contains the mouth, beaks, radula and various glands.buccal systembuccal massMuscular bulb at the beginning of the digestive system that contains the mouth, beaks, radula and various glands.http://tolweb.org/accessory/Cephalopod_Digestive_System?acc_id=1993The muscular membrane that connects the buccal supports and together with the supports, forms the buccal crown. The pigmentation of the buccal membrane often differs from that of the adjacent oral surfaces of the arms.buccal membraneThe muscular membrane that connects the buccal supports and together with the supports, forms the buccal crown. The pigmentation of the buccal membrane often differs from that of the adjacent oral surfaces of the arms.http://tolweb.org/accessory/Cephalopod_Brachial_and_Buccal_Crowns?acc_id=1957Small but normal suckers that are present on the oral surface of the buccal supports of some decapodiforms (bathyteuthid families, some loliginids and some sepiids).buccal suckerSmall but normal suckers that are present on the oral surface of the buccal supports of some decapodiforms (bathyteuthid families, some loliginids and some sepiids).http://tolweb.org/accessory/Cephalopod_Brachial_and_Buccal_Crowns?acc_id=1957A spermatophore receptacle found in some sepiolids and consisting of folded glandular epithelium of the lining of the mantle cavity just anterior to the oviduct opening.bursa copulatrixA spermatophore receptacle found in some sepiolids and consisting of folded glandular epithelium of the lining of the mantle cavity just anterior to the oviduct opening.http://tolweb.org/accessory/Cephalopoda_Glossary?acc_id=587The sac-like, thin-walled posterior portion of the caecum that lacks the internal, ciliated leaflets characteristic of the anterior portion of the caecum.caecal sacThe sac-like, thin-walled posterior portion of the caecum that lacks the internal, ciliated leaflets characteristic of the anterior portion of the caecum.http://tolweb.org/accessory/Cephalopod_Digestive_System?acc_id=1993Region of the digestive tract of all cephalopods between the stomach and intestine. It is the primary site of food absorption.caecumRegion of the digestive tract of all cephalopods between the stomach and intestine. It is the primary site of food absorption.http://tolweb.org/accessory/Cephalopod_Digestive_System?acc_id=1993Composed of calcium carbonate (CaCO3)calcareousComposed of calcium carbonate (CaCO3)http://tolweb.org/accessory/Cephalopoda_Glossary?acc_id=587The conical papilla of the end-organ of the hectocotylus in many incirrate octopods. It is located at the distal termination of the sperm groove and usually lies adjacent to the last arm sucker.calamusThe conical papilla of the end-organ of the hectocotylus in many incirrate octopods. It is located at the distal termination of the sperm groove and usually lies adjacent to the last arm sucker.http://tolweb.org/accessory/Cephalopoda_Glossary?acc_id=587Structure in the spermatophore that allows adhesion of the discharged spermatophore to a female.cement bodyStructure in the spermatophore that allows adhesion of the discharged spermatophore to a female.http://tolweb.org/accessory/Cephalopod_Spermatophore_Terminology?acc_id=1972Suckers in the locking apparatus at the base of the club.carpal suckerSuckers in the locking apparatus at the base of the club.http://tolweb.org/accessory/Cephalopod_Tentacle_Terminology?acc_id=1962Knobs in the locking apparatus at the base of the club.carpal knobKnobs in the locking apparatus at the base of the club.http://tolweb.org/accessory/Cephalopod_Tentacle_Terminology?acc_id=1962The region of the tentacle that contains the carpal locking-apparatus carpusThe region of the tentacle that contains the carpal locking-apparatus http://tolweb.org/accessory/Cephalopod_Tentacle_Terminology?acc_id=1962The region at the base of the tentacular club which has small suckers and knobs. The carpal suckers and knobs of one tentacle can adhere to their counterparts on the opposite tentacle which, thereby, holds the clubs together at their bases.proximal locking-apparatuscarpal locking apparatusThe region at the base of the tentacular club which has small suckers and knobs. The carpal suckers and knobs of one tentacle can adhere to their counterparts on the opposite tentacle which, thereby, holds the clubs together at their bases.http://tolweb.org/accessory/Cephalopoda_Glossary?acc_id=587Rigid cartilagenous spines, with one or several cusps, in the skin of certain squids and octopods.cartilaginous tubercleRigid cartilagenous spines, with one or several cusps, in the skin of certain squids and octopods.http://tolweb.org/accessory/Cephalopoda_Glossary?acc_id=587Cartilage surrounding the posterior part of the brain of cephalopods and generally encompasing the statocysts. Anteriorly the cartilage thins into facia making a well-defined limit difficult to establish. The cartilage has a large central foramen through which the esophagus passes and minor foramina for nerves and blood vessels.cephalic cartilageCartilage surrounding the posterior part of the brain of cephalopods and generally encompasing the statocysts. Anteriorly the cartilage thins into facia making a well-defined limit difficult to establish. The cartilage has a large central foramen through which the esophagus passes and minor foramina for nerves and blood vessels.http://tolweb.org/accessory/Cephalopoda_Glossary?acc_id=587Large vein that drains the head and lies on the ventral surface of the visceral sac, along side or dorsal to the intestine. The cephalic vein terminates by dividing into the two vena cavae, each of which passes through the &quot;kidney&quot; (nephridium), the branchial heart and into the gill.cephalic veinLarge vein that drains the head and lies on the ventral surface of the visceral sac, along side or dorsal to the intestine. The cephalic vein terminates by dividing into the two vena cavae, each of which passes through the &quot;kidney&quot; (nephridium), the branchial heart and into the gill.http://tolweb.org/accessory/Cephalopoda_Glossary?acc_id=587A mucopolysaccharide that is the major component of the cuticle (exoskeleton) of arthropods and a major component of the gladius and beaks of cephalopods (also found in many other phyla).chitinA mucopolysaccharide that is the major component of the cuticle (exoskeleton) of arthropods and a major component of the gladius and beaks of cephalopods (also found in many other phyla).http://tolweb.org/accessory/Cephalopoda_Glossary?acc_id=587A pigment cell. In cephalopods the chromatophore is part of an organ composed of numerous cells including many slender muscle cells. Under nervous control, the muscles rapidly expand and flatten the pigment cell which spreads the pigment over a relatively broad area.chromatophoreA pigment cell. In cephalopods the chromatophore is part of an organ composed of numerous cells including many slender muscle cells. Under nervous control, the muscles rapidly expand and flatten the pigment cell which spreads the pigment over a relatively broad area.http://tolweb.org/accessory/Cephalopod_Chromatophore?acc_id=2038A circular muscle found in the suckers of most sepioids and loliginids that surrounds the sucker at the base of the horny ring.circularis muscleA circular muscle found in the suckers of most sepioids and loliginids that surrounds the sucker at the base of the horny ring.http://tolweb.org/accessory/Cephalopoda_Glossary?acc_id=587The male reproductive tract of cirrates does not make typical spermatophores. As a result, the tract differs greatly from that of other coleoid cephalopods. cirrate male reproductive systemThe male reproductive tract of cirrates does not make typical spermatophores. As a result, the tract differs greatly from that of other coleoid cephalopods. http://tolweb.org/accessory/Cirrate_Male_Reproductive_Tract?acc_id=1486Measurements used in describing cirrates differ somewhat from other cephalopods. cirrate octopod measurementsMeasurements used in describing cirrates differ somewhat from other cephalopods. http://tolweb.org/accessory/Cirrate_Measurements_and_Indices?acc_id=1487Muscular, conical structures that arise from the sides of the arms of some octopodiforms. Cirri are homologous with trabeculae of decapodiforms.arm cirrusMuscular, conical structures that arise from the sides of the arms of some octopodiforms. Cirri are homologous with trabeculae of decapodiforms.http://tolweb.org/accessory/Cephalopoda_Glossary?acc_id=587An internal body cavity of mesodermal orgin that is lined by an epithelium. Cephalopods have two coeloms, the visceropericardial coelom and the nephridial coelom.cephalopod coelomAn internal body cavity of mesodermal orgin that is lined by an epithelium. Cephalopods have two coeloms, the visceropericardial coelom and the nephridial coelom.http://tolweb.org/accessory/Cephalopoda_Glossary?acc_id=587Muscular structure extending from the nuchal cartilage to the funnel that forms a one-way valve that lets water enter the mantle cavity but closes as the mantle contracts thereby forcing exhalent water out through the funnel.collarMuscular structure extending from the nuchal cartilage to the funnel that forms a one-way valve that lets water enter the mantle cavity but closes as the mantle contracts thereby forcing exhalent water out through the funnel.http://tolweb.org/accessory/Cephalopoda_Glossary?acc_id=587Structures that alter the color of bioluminescent light.photophore color filterStructures that alter the color of bioluminescent light.http://tolweb.org/accessory/Cephalopoda_Glossary?acc_id=587The cup or cone-shaped posterior end of the gladius or cuttlebone of some cephalopods. It is not formed by the infolding of the vanes.conus flagconeconusThe cup or cone-shaped posterior end of the gladius or cuttlebone of some cephalopods. It is not formed by the infolding of the vanes.http://tolweb.org/accessory/Cephalopoda_Glossary?acc_id=587Lateral portions of the gladius that are continuous posteriorly with the primary conus or its remnant and laterally with the edges of the vanes.conus fieldLateral portions of the gladius that are continuous posteriorly with the primary conus or its remnant and laterally with the edges of the vanes.http://tolweb.org/accessory/Cephalopod_Gladius_Terminology?acc_id=1955Smooth, thin, turgid, transparent skin without muscles that covers the eyes to protect the eye lenses of incirrate octopods and some decapodiforms.corneaSmooth, thin, turgid, transparent skin without muscles that covers the eyes to protect the eye lenses of incirrate octopods and some decapodiforms.http://tolweb.org/accessory/Cephalopod_Cornea?acc_id=2057The production of bioluminescent light by an animal to conceal its silhouette against the downwelling light. The process can allow an aninmal to become virtually invisible under dim directional light.counterilluminationThe production of bioluminescent light by an animal to conceal its silhouette against the downwelling light. The process can allow an aninmal to become virtually invisible under dim directional light.http://tolweb.org/accessory/Cephalopoda_Glossary?acc_id=587In loliginids a protective membrane on the hectocotylized arm can fuse with the adjacent suckerless papillae (former sucker stalks) to form a crest on the dorsal or ventral margins such that the original form of the papillae is obscured.crest of hectocotylusIn loliginids a protective membrane on the hectocotylized arm can fuse with the adjacent suckerless papillae (former sucker stalks) to form a crest on the dorsal or ventral margins such that the original form of the papillae is obscured.http://tolweb.org/accessory/Cephalopoda_Glossary?acc_id=587Expansion (i.e. a broading or a side pocket) of the esophagus for storing food. Present in <strong>Nautilus</strong> and most octopodiforms.cropExpansion (i.e. a broading or a side pocket) of the esophagus for storing food. Present in <strong>Nautilus</strong> and most octopodiforms.http://tolweb.org/accessory/Cephalopod_Digestive_System?acc_id=1993Radula in which the lateral teeth are multicuspid.ctenoglossan radulaRadula in which the lateral teeth are multicuspid.http://tolweb.org/accessory/Cephalopoda_Glossary?acc_id=587The peculiar posterior end of the histioteuthis gladius that is rolled into a coil.cupped coilThe peculiar posterior end of the histioteuthis gladius that is rolled into a coil.http://tolweb.org/accessory/Cephalopoda_Glossary?acc_id=587A point or projection on a tooth of the radula or on a cartilagenous tubercule in the skin.cuspA point or projection on a tooth of the radula or on a cartilagenous tubercule in the skin.http://tolweb.org/accessory/Cephalopoda_Glossary?acc_id=587A calcareous oblong supporting part of the mantle of cuttlefishessepioncuttleboneA calcareous oblong supporting part of the mantle of cuttlefisheshttp://www.sil.si.edu/smithsoniancontributions/zoology/pdf_hi/sctz-0513.pdfThe narrow, distal portion of the tentacular club of most decapodiforms. In squids the dactylus is usually characterized by the ventral expansion of the club and the absence of a dorsal protective membrane.dactylusThe narrow, distal portion of the tentacular club of most decapodiforms. In squids the dactylus is usually characterized by the ventral expansion of the club and the absence of a dorsal protective membrane.http://tolweb.org/accessory/Cephalopod_Tentacle_Terminology?acc_id=1962Living close to the ocean floor.demersalLiving close to the ocean floor.http://tolweb.org/accessory/Cephalopoda_Glossary?acc_id=587A half-gill formed from all the primary gill lamellae on one side of the gill.demibranchA half-gill formed from all the primary gill lamellae on one side of the gill.http://tolweb.org/accessory/Cephalopoda_Glossary?acc_id=587Vertical animal migration during twilight. Many mesopelagic animals migrate at sunrise from near-surface waters to spend the day at greater depths then return to shallow depths at sunset where they spend the night. Some animals migrate vertically over 1000 m others migrate less than 100 m.diel vertical migrationVertical animal migration during twilight. Many mesopelagic animals migrate at sunrise from near-surface waters to spend the day at greater depths then return to shallow depths at sunset where they spend the night. Some animals migrate vertically over 1000 m others migrate less than 100 m.http://tolweb.org/accessory/Cephalopoda_Glossary?acc_id=587Primary organ in cephalopods that secretes digestive enzymes. It is also important in absorption and excretion.digestive glandPrimary organ in cephalopods that secretes digestive enzymes. It is also important in absorption and excretion.http://tolweb.org/accessory/Cephalopod_Digestive_System?acc_id=1993Outpockets of the ducts leading from the digestive gland that are covered with glandular epithelium.digestive gland duct appendages (digda)Outpockets of the ducts leading from the digestive gland that are covered with glandular epithelium.http://tolweb.org/accessory/Cephalopod_Digestive_System?acc_id=1993An extension of the oviducal gland in octopods that often has the same general appearance as the oviduct proximal to the oviducal gland.distal oviductAn extension of the oviducal gland in octopods that often has the same general appearance as the oviduct proximal to the oviducal gland.http://tolweb.org/accessory/Cephalopoda_Glossary?acc_id=587Peculiar paralarval stage of the Chiroteuthidae. The paralarva is very slender and can reach a large size.doratopsisdoratopsis stagePeculiar paralarval stage of the Chiroteuthidae. The paralarva is very slender and can reach a large size.http://tolweb.org/accessory/Chiroteuthid_Doratopsis_Stage?acc_id=656Dorsal portion of the mantle cavity that completely surrounds the viscera in octopods. In decapodiforms and <strong>Vampyroteuthis</strong> the viscera are fused to the mantle and shell dorsally and the mantle cavity lies lateral and ventral to the viscera. dorsal mantle cavityDorsal portion of the mantle cavity that completely surrounds the viscera in octopods. In decapodiforms and <strong>Vampyroteuthis</strong> the viscera are fused to the mantle and shell dorsally and the mantle cavity lies lateral and ventral to the viscera. http://tolweb.org/accessory/Cephalopoda_Glossary?acc_id=587vein carrying blood away from an organ.efferent veinvein carrying blood away from an organ.http://tolweb.org/accessory/Cephalopoda_Glossary?acc_id=587nerve carring impulses away from the brain or specific ganglia.efferent nervenerve carring impulses away from the brain or specific ganglia.http://tolweb.org/accessory/Cephalopoda_Glossary?acc_id=587A large number of eggs encapsulated in a gelatinous matrix or a large number of such structures that are attached together. The egg mass of an oceanic squid can be a large, fragile gelatinous ball carrying many thousands of eggs. In contrast, the egg mass of a neritic squid (loliginid) can be composed of very tough capsules each carrying several hundred eggs with many capsules attached together at their bases and to the substrate to form an egg mass.egg caseegg massA large number of eggs encapsulated in a gelatinous matrix or a large number of such structures that are attached together. The egg mass of an oceanic squid can be a large, fragile gelatinous ball carrying many thousands of eggs. In contrast, the egg mass of a neritic squid (loliginid) can be composed of very tough capsules each carrying several hundred eggs with many capsules attached together at their bases and to the substrate to form an egg mass.http://tolweb.org/accessory/Cephalopoda_Glossary?acc_id=587Portion of the spermatophore involved in the eversion of the sperm mass.ejaculatory apparatusPortion of the spermatophore involved in the eversion of the sperm mass.http://tolweb.org/accessory/Cephalopod_Spermatophore_Terminology?acc_id=1972The tip of the hectocotylus in incirrate octopods consisting of a calamus and ligula presumably for manipulating the spermatophore during copulation.end organ of hectocotylusterminal organend organThe tip of the hectocotylus in incirrate octopods consisting of a calamus and ligula presumably for manipulating the spermatophore during copulation.http://tolweb.org/accessory/Cephalopoda_Glossary?acc_id=587The pigmentation that is contained in epithelial cells which are unable to change their shape. Color in most cephalopods, however, is due to pigment granules that are contained in specialized organs, the chromatophore organs, that can change shape rapidly under nervous control. See chromatophores.epithelial pigmentationThe pigmentation that is contained in epithelial cells which are unable to change their shape. Color in most cephalopods, however, is due to pigment granules that are contained in specialized organs, the chromatophore organs, that can change shape rapidly under nervous control. See chromatophores.http://tolweb.org/accessory/Cephalopoda_Glossary?acc_id=587Small pore just anterior to the cornea in some decapodiforms. The pore is the remnant of the large eye opening of oegopsids and connects fluid between the lens and the cornea with the exterior environment.eye poreSmall pore just anterior to the cornea in some decapodiforms. The pore is the remnant of the large eye opening of oegopsids and connects fluid between the lens and the cornea with the exterior environment.http://tolweb.org/accessory/Cephalopoda_Glossary?acc_id=587Indentation, often complex, of the anterior margin of the eyelid. optic sinusorbital sinuseyelid sinusIndentation, often complex, of the anterior margin of the eyelid. http://tolweb.org/accessory/Cephalopod_Eyelid_Sinus?acc_id=1994The angle between the longitudinal axis of the mantle and the posterior border of one fin.fin angleThe angle between the longitudinal axis of the mantle and the posterior border of one fin.http://tolweb.org/accessory/Cephalopoda_Glossary?acc_id=587A fin attaches to the shell, the mantle, the opposite fin or some combination of these. fin attachmentA fin attaches to the shell, the mantle, the opposite fin or some combination of these. http://tolweb.org/accessory/Cephalopod_Fin_Attachment?acc_id=1974Cartilage associated with the fins of all fin-bearing cephalopods. fin cartilageCartilage associated with the fins of all fin-bearing cephalopods. http://tolweb.org/accessory/Cephalopoda_Fin_Cartilage?acc_id=1969This measurement varies in different major taxa. fin lengthThis measurement varies in different major taxa. http://tolweb.org/accessory/Cephalopod_Fin_Length?acc_id=2055The portion of a fin that extends anteriorly from the fin's anterior point of attachment or posteriorly from the fin's posterior point of attachment. This is often called the &quot;free&quot; lobe.fin lobeThe portion of a fin that extends anteriorly from the fin's anterior point of attachment or posteriorly from the fin's posterior point of attachment. This is often called the &quot;free&quot; lobe.http://tolweb.org/accessory/Composite_Squid?acc_id=1936Fins are located anterior to the termination of the muscular mantle (subterminal position) or mostly posterior to it (terminal position) or somewhere inbetween. fin positionFins are located anterior to the termination of the muscular mantle (subterminal position) or mostly posterior to it (terminal position) or somewhere inbetween. http://tolweb.org/accessory/Cephalopod_Fin_Position?acc_id=2041Fins are classified, somewhat arbitrarily, by their shape as Sagittate, Rhomboid, Circular/Elliptical, Lanceolate, Ear-shaped, Ribbed, Lobate or skirt-like. fin shapeFins are classified, somewhat arbitrarily, by their shape as Sagittate, Rhomboid, Circular/Elliptical, Lanceolate, Ear-shaped, Ribbed, Lobate or skirt-like. http://tolweb.org/accessory/Decapodiform_Fin_Shapes?acc_id=2029A muscular flap that arises along the lateral or dorsolateral surface of the mantle of some cephalopods. Used for locomotion, steering and stabilizationfinTransverse membranous fold of skin that forms a pocket in the funnel groove of ommastrephid squids.foveolaTransverse membranous fold of skin that forms a pocket in the funnel groove of ommastrephid squids.http://tolweb.org/accessory/Cephalopoda_Glossary?acc_id=587The portion of a fin that extends anteriorly from the fin's anterior point of attachment or posteriorly from the fin's posterior point of attachment.obsolete free fin lobetrueThe portion of a fin that extends anteriorly from the fin's anterior point of attachment or posteriorly from the fin's posterior point of attachment.http://tolweb.org/accessory/Cephalopoda_Glossary?acc_id=587The ventral, muscular tube through which water is expelled from the mantle cavity. The funnel is thought to have evolved from the molluscan foot.siphonhyponomefunnelThe ventral, muscular tube through which water is expelled from the mantle cavity. The funnel is thought to have evolved from the molluscan foot.http://tolweb.org/accessory/Cephalopoda_Glossary?acc_id=587Depression on the posteroventral surface of the head in which the funnel lies. Most distinct in some squids.funnel grooveDepression on the posteroventral surface of the head in which the funnel lies. Most distinct in some squids.http://tolweb.org/accessory/Cephalopoda_Glossary?acc_id=587The funnel component (generally cartilagenous) of a locking mechanism between the funnel and mantle. This lock, depending on its form, can either limit all movement between the funnel and mantle or allow just anterior-posterior slipping. See Mantle locking-apparatus.funnel locking apparatusfunnel locking-cartilagefunnel-mantle locking-apparatusThe funnel component (generally cartilagenous) of a locking mechanism between the funnel and mantle. This lock, depending on its form, can either limit all movement between the funnel and mantle or allow just anterior-posterior slipping. See Mantle locking-apparatus.http://tolweb.org/accessory/Cephalopod_Funnel_Locking-Apparatus?acc_id=1973The glandular structures on the internal dorsal and ventral surfaces of the funnel.funnel organThe glandular structures on the internal dorsal and ventral surfaces of the funnel.http://tolweb.org/accessory/Cephalopoda_Glossary?acc_id=587Large muscles that attach to the corners of the funnel and run posteriorly to attach to the sides of the shell sac (generally near the base of the gills) or, in a some species, insert on the mantle wall.funnel retractor muscleLarge muscles that attach to the corners of the funnel and run posteriorly to attach to the sides of the shell sac (generally near the base of the gills) or, in a some species, insert on the mantle wall.http://tolweb.org/accessory/Cephalopoda_Glossary?acc_id=587Semicircular muscular flap extending from and continuous with the posterodorsal funnel wall. The funnel valve apparently acts as a one-way valve to prevent inspiration of water through the funnel when mantle expansion draws in water to pass over the gills for respiration. A funnel valve in absent in octopods and some squids.funnel valveSemicircular muscular flap extending from and continuous with the posterodorsal funnel wall. The funnel valve apparently acts as a one-way valve to prevent inspiration of water through the funnel when mantle expansion draws in water to pass over the gills for respiration. A funnel valve in absent in octopods and some squids.http://tolweb.org/accessory/Cephalopoda_Glossary?acc_id=587Primary organ for the exchange of respiratory gases between blood and sea water.gillPrimary organ for the exchange of respiratory gases between blood and sea water.http://tolweb.org/articles/?article_id=4200A complex gill leaflet that extends perpendicular to the axis of the gill and contains the respiratory epithelium. The lamella contains further subdivisions, the secondary and tertiary lamellae. In octopods the number of lamellae is a taxonomic character.gill lamellaeprimary lamellagill lamellaA complex gill leaflet that extends perpendicular to the axis of the gill and contains the respiratory epithelium. The lamella contains further subdivisions, the secondary and tertiary lamellae. In octopods the number of lamellae is a taxonomic character.http://tolweb.org/accessory/Cephalopoda_Glossary?acc_id=587The chitinous remnant of the shell in many decapodiforms and <strong>Vampyroteuthis</strong>. It is generally feather-shaped and lies in the dorsal mid-line of the body along the full length of the mantle. The gladius lies within the shell sac which secretes it.internal gladiusgladiipengladiushttp://www.sil.si.edu/smithsoniancontributions/zoology/pdf_hi/sctz-0513.pdfThe chitinous remnant of the shell in many decapodiforms and <strong>Vampyroteuthis</strong>. It is generally feather-shaped and lies in the dorsal mid-line of the body along the full length of the mantle. The gladius lies within the shell sac which secretes it.http://tolweb.org/accessory/Cephalopod_Gladius_Terminology?acc_id=1955Gills of some cirrate octopods with broad primary lamellae whose arrangement looks similar to half of an orange. half-orange gillGills of some cirrate octopods with broad primary lamellae whose arrangement looks similar to half of an orange. http://tolweb.org/accessory/Cephalopoda_Glossary?acc_id=587Young cephalopod that has just hatched from the egg.hatchlinghatchling stageYoung cephalopod that has just hatched from the egg.http://tolweb.org/accessory/Cephalopoda_Glossary?acc_id=587.head-mantle fusion.http://tolweb.org/accessory/Cephalopod_Dorsal_Head-Mantle_Fusion?acc_id=2020The modified arm in males used for transferring spermatophores to the female. In incirrates the hectocotylus is one member of arm pair III while in decapodiforms frequently one or both members of arm pair IV are modified. Many species of coleoid cephalopods lack a hectocotylus.hectoctylized armhectocotylusWikipediaThe modified arm in males used for transferring spermatophores to the female. In incirrates the hectocotylus is one member of arm pair III while in decapodiforms frequently one or both members of arm pair IV are modified. Many species of coleoid cephalopods lack a hectocotylus.Wikipedia:Hectocotylushttp://tolweb.org/accessory/Cephalopoda_Glossary?acc_id=587Radula with more than one cusp on the rhachidian tooth and, usually, the first lateral tooth.heterodont radulaRadula with more than one cusp on the rhachidian tooth and, usually, the first lateral tooth.http://tolweb.org/accessory/Cephalopoda_Glossary?acc_id=587Radula with a single cusp on all teeth.homodont radulaRadula with a single cusp on all teeth.http://tolweb.org/accessory/Cephalopoda_Glossary?acc_id=587The single specimen designated to represent a species name. It is an international standard of reference that provides objectivity for the species name.obsolete holotypetrueThe single specimen designated to represent a species name. It is an international standard of reference that provides objectivity for the species name.http://tolweb.org/accessory/Cephalopoda_Glossary?acc_id=587Horny structure that looks like a single claw and is derived from the inner sucker ring in some decapodiforms. Hooks may be found on the arms and/or tentacular clubs of squid. The relative advantage of hooks vs toothed rings is uncertain.hookHorny structure that looks like a single claw and is derived from the inner sucker ring in some decapodiforms. Hooks may be found on the arms and/or tentacular clubs of squid. The relative advantage of hooks vs toothed rings is uncertain.http://tolweb.org/accessory/Cephalopod_Hooks?acc_id=1983Septa, extending the length of the arm (i.e., parallel to the arm axis), that roughly divides the arm into oral and aboral regions. This feature is a characteristic of the arms of cirrate octopods and the incirrate octopods of the family Bolitaenidae. The functional significance is unknown.horizontal arm septumSepta, extending the length of the arm (i.e., parallel to the arm axis), that roughly divides the arm into oral and aboral regions. This feature is a characteristic of the arms of cirrate octopods and the incirrate octopods of the family Bolitaenidae. The functional significance is unknown.http://tolweb.org/accessory/Cephalopoda_Glossary?acc_id=587A chitinous ring that encircles a sucker. Found in cuttlefishes and squidshorny ring of suckersucker ringA system of lobes in octopod brains: the paired posterior buccal, lateral inferior frontal and subfrontal lobes, and the single median inferior frontal lobe. They form a functional unit concerned with the chemotactile information from the arms and its use.inferior frontal lobe systemA system of lobes in octopod brains: the paired posterior buccal, lateral inferior frontal and subfrontal lobes, and the single median inferior frontal lobe. They form a functional unit concerned with the chemotactile information from the arms and its use.http://tolweb.org/accessory/Cephalopoda_Glossary?acc_id=587Exposed flat outer ring that forms the adhesive surface of the suckerinfundibilumExposed flat outer ring that forms the adhesive surface of the suckerhttp://www.sil.si.edu/smithsoniancontributions/zoology/pdf_hi/sctz-0513.pdfOrgan composed of a gland that secretes ink, a sac that stores ink and a duct that connects it to the rectum. The ink sac generally appears black from the outside although it may be covered by silvery tissue in some species.ink sacOrgan composed of a gland that secretes ink, a sac that stores ink and a duct that connects it to the rectum. The ink sac generally appears black from the outside although it may be covered by silvery tissue in some species.http://tolweb.org/accessory/Cephalopoda_Glossary?acc_id=587This is the typical method of fast swimming in cephalopods. During jet propulsion, water is taken into the mantle cavity by expansion of the mantle. Water enters laterally at the sides of the head, passes over the collar, over the gills and leaves through the funnel when the mantle contracts. Mantle contraction causes water pressure in the mantle cavity to increase and forces the collar against the mantle wall. The collar, therefore, acts as a one-way valve to prevents water from leaving by the same route that it entered. The ventral wall of the funnel presses against the mantle during mantle contraction and seals that opening as well. Water, therefore, is forced through the funnel and out the funnel orifice. The force provided by the water leaving the funnel can be directed by movements of the funnel. Typically the water leaves the funnel anteriorly causing the cephalopod to jet backward (e.g. when escaping a predator) or the funnel is directed posteriorly causing the water to leave posteriorly and the animal to jet anteriorly (e.g. when pouncing on a prey). Some species are able to glide via this method.jet propulsionThis is the typical method of fast swimming in cephalopods. During jet propulsion, water is taken into the mantle cavity by expansion of the mantle. Water enters laterally at the sides of the head, passes over the collar, over the gills and leaves through the funnel when the mantle contracts. Mantle contraction causes water pressure in the mantle cavity to increase and forces the collar against the mantle wall. The collar, therefore, acts as a one-way valve to prevents water from leaving by the same route that it entered. The ventral wall of the funnel presses against the mantle during mantle contraction and seals that opening as well. Water, therefore, is forced through the funnel and out the funnel orifice. The force provided by the water leaving the funnel can be directed by movements of the funnel. Typically the water leaves the funnel anteriorly causing the cephalopod to jet backward (e.g. when escaping a predator) or the funnel is directed posteriorly causing the water to leave posteriorly and the animal to jet anteriorly (e.g. when pouncing on a prey). Some species are able to glide via this method.Wikipedia:Ommastrephidaehttp://tolweb.org/accessory/Cephalopod_Jet_Propulsion?acc_id=2060A muscular vane that extends dorsally from the aboral surface of the tentacular club of many species.swimming membraneclubkeelA muscular vane that extends dorsally from the aboral surface of the tentacular club of many species.http://tolweb.org/accessory/Cephalopoda_Glossary?acc_id=587Muscles that support the lateral attachment of the funnel to the head. lateral funnel adductor muscleMuscles that support the lateral attachment of the funnel to the head. http://tolweb.org/accessory/Cephalopod_Lateral_Funnel_Adductor?acc_id=1963The keels of arms IV are offset laterally and often enlarged to fully or partially conceal, protect or encase the adjacent tentacles. The latter function is most fully developed in the chiroteuthids and mastigoteuthids.tentacular sheathlateral membrane of arm IVThe keels of arms IV are offset laterally and often enlarged to fully or partially conceal, protect or encase the adjacent tentacles. The latter function is most fully developed in the chiroteuthids and mastigoteuthids.http://tolweb.org/accessory/Cephalopod_Brachial_and_Buccal_Crowns?acc_id=1957tentacular sheathhttp://tolweb.org/accessory/Cephalopod_Brachial_and_Buccal_Crowns?acc_id=1957Sensory structure analogous to the lateral-line of fishes. The lateral-line analogue, which senses vibrations transmitted by the seawater, is located along a series of lines on the dorsal surface of the head with some sensory cells extending onto the bases of the arms.lateral-line analogueSensory structure analogous to the lateral-line of fishes. The lateral-line analogue, which senses vibrations transmitted by the seawater, is located along a series of lines on the dorsal surface of the head with some sensory cells extending onto the bases of the arms.http://tolweb.org/accessory/Cephalopoda_Glossary?acc_id=587Structure in a photophore that can focus or disperse bioluminescent light.photophore lensStructure in a photophore that can focus or disperse bioluminescent light.http://tolweb.org/accessory/Cephalopoda_Glossary?acc_id=587Structures in a photophores that direct light via internal reflection.light guidesStructures in a photophores that direct light via internal reflection.http://tolweb.org/accessory/Cephalopod_Photophore_Terminology?acc_id=2015The portion of the sucker-free end-organ of the hectocotylus of many incirrate octopods that is generally elongate and longitudinally grooved. The ligula in octopodids is often spatulate in shape with transverse ridges. Spermatophores transferred along the sperm groove of the hectocotylus presumably enter the ligula which assists in their transfer to the female. Details of the use of the ligula are unknown.ligulaThe portion of the sucker-free end-organ of the hectocotylus of many incirrate octopods that is generally elongate and longitudinally grooved. The ligula in octopodids is often spatulate in shape with transverse ridges. Spermatophores transferred along the sperm groove of the hectocotylus presumably enter the ligula which assists in their transfer to the female. Details of the use of the ligula are unknown.http://tolweb.org/accessory/Cephalopoda_Glossary?acc_id=587Two concentric muscular, glandular rings of skin that surround the mouth and beaks.lipTwo concentric muscular, glandular rings of skin that surround the mouth and beaks.http://tolweb.org/accessory/Cephalopoda_Glossary?acc_id=587Largest and most recently formed chamber of the <strong>Nautilus</strong> shell (also refers to numerous shells of fossil cephalopods) in which the animal resides.living chamberLargest and most recently formed chamber of the <strong>Nautilus</strong> shell (also refers to numerous shells of fossil cephalopods) in which the animal resides.http://tolweb.org/accessory/Cephalopoda_Glossary?acc_id=587Continuation of the carpal locking apparatus down the oral face of the tentacular stalk. locking-apparatus of tentacular stalkContinuation of the carpal locking apparatus down the oral face of the tentacular stalk. http://tolweb.org/accessory/Cephalopoda_Glossary?acc_id=587The mantle component (usually fibrous) of the structure that &quot;locks&quot; the mantle to the funnel. This lock, depending on its form, can either restrict all movement between the funnel and mantle or allow just an anterior/posterior slippage.mantle locking cartilagemantle locking-apparatusThe mantle component (usually fibrous) of the structure that &quot;locks&quot; the mantle to the funnel. This lock, depending on its form, can either restrict all movement between the funnel and mantle or allow just an anterior/posterior slippage.http://tolweb.org/accessory/Cephalopoda_Glossary?acc_id=587(ML) - The standard measure of length in coleoid cephalopods. In decapodiforms ML is measured along the dorsal midline from the mantle margin to the posterior tip of the body, excluding long tails. In octopodiforms ML is measured from a line joining the midpoint of the eyes rather than the anterior mantle margin since the latter is obscured by the head/mantle fusion.mantle length(ML) - The standard measure of length in coleoid cephalopods. In decapodiforms ML is measured along the dorsal midline from the mantle margin to the posterior tip of the body, excluding long tails. In octopodiforms ML is measured from a line joining the midpoint of the eyes rather than the anterior mantle margin since the latter is obscured by the head/mantle fusion.http://tolweb.org/accessory/Cephalopoda_Glossary?acc_id=587A anteroposterior septum that connects the mantle wall with the visceral sac along the midline in the ventral mantle cavity. The ventral mantle artery runs along the anterior end of this septum. abdominal septummantle septumA anteroposterior septum that connects the mantle wall with the visceral sac along the midline in the ventral mantle cavity. The ventral mantle artery runs along the anterior end of this septum. http://tolweb.org/accessory/Cephalopoda_Glossary?acc_id=587The proximal, broad portion of the tentacular club. In squids the manus is generally equally expanded on both lateral margins and often includes enlarged suckers.manusmanus of tentacular clubThe proximal, broad portion of the tentacular club. In squids the manus is generally equally expanded on both lateral margins and often includes enlarged suckers.http://tolweb.org/accessory/Cephalopod_Tentacle_Terminology?acc_id=1962In cephalopods this term refers to sexual maturity which is determined for females by the presence of ova (mature eggs) free in the coelom or oviducts, and for males by the presence of spermatophores in Needham's sac.mature stageIn cephalopods this term refers to sexual maturity which is determined for females by the presence of ova (mature eggs) free in the coelom or oviducts, and for males by the presence of spermatophores in Needham's sac.http://tolweb.org/accessory/Cephalopoda_Glossary?acc_id=587A major structure in molluscan morphology. In gastropods the foot is the muscular sole that the animal crawls with. In cephalopods the funnel, and possibly the arms and tentacles are derived from the molluscan foot. The evolutionary origin of the latter is still uncertain. They may represent outgrowths of the head (favored by anatomical evidence: nerve connections) or modifications of the molluscan foot that have migrated around the mouth (favored by embryological evidence: migration of arm primordia).footmolluscan footA major structure in molluscan morphology. In gastropods the foot is the muscular sole that the animal crawls with. In cephalopods the funnel, and possibly the arms and tentacles are derived from the molluscan foot. The evolutionary origin of the latter is still uncertain. They may represent outgrowths of the head (favored by anatomical evidence: nerve connections) or modifications of the molluscan foot that have migrated around the mouth (favored by embryological evidence: migration of arm primordia).http://tolweb.org/accessory/Cephalopoda_Glossary?acc_id=587The region separating the posterior end of the cephalic cartilage and the collar. Only those cephalopods with elongate heads (e.g., chiroteuthids) have distinct necks.neckThe region separating the posterior end of the cephalic cartilage and the collar. Only those cephalopods with elongate heads (e.g., chiroteuthids) have distinct necks.http://tolweb.org/accessory/Cephalopoda_Glossary?acc_id=587In males, the large storage sac for spermatophores that is an expanded region of the genital duct at the base of the penis.spermatophore sacspermatophoric sacNeedham's sacIn males, the large storage sac for spermatophores that is an expanded region of the genital duct at the base of the penis.http://tolweb.org/accessory/Cephalopoda_Glossary?acc_id=587The cavity of the renal sac. It connects with the exterior via the renal pore and with the visceropericardial coelom via a pair of slender ducts from the latter.nephridial coelomThe cavity of the renal sac. It connects with the exterior via the renal pore and with the visceropericardial coelom via a pair of slender ducts from the latter.http://tolweb.org/accessory/Cephalopoda_Glossary?acc_id=587Large glandular structures found in decapodiforms and <strong>Nautilus</strong> that lie in and open directly into the mantle cavity. The glands are composed of numerous lamellae that are involved in secretion of egg cases or the jelly of egg masses.nidamental glandLarge glandular structures found in decapodiforms and <strong>Nautilus</strong> that lie in and open directly into the mantle cavity. The glands are composed of numerous lamellae that are involved in secretion of egg cases or the jelly of egg masses.http://tolweb.org/accessory/Cephalopoda_Glossary?acc_id=587An oblong cartilaginou plate on the posterodorsal surface of the head of most squids and cuttlefishes that articulates with a complementary structure on the inner surface of the anterodorsal surface of the mantlenuchal cartilageAn oblong cartilaginou plate on the posterodorsal surface of the head of most squids and cuttlefishes that articulates with a complementary structure on the inner surface of the anterodorsal surface of the mantlehttp://www.sil.si.edu/smithsoniancontributions/zoology/pdf_hi/sctz-0513.pdfSee Occipital crest.nuchal crestSee Occipital crest.http://tolweb.org/accessory/Cephalopoda_Glossary?acc_id=587See occipital membrane.nuchal membraneSee occipital membrane.http://tolweb.org/accessory/Cephalopoda_Glossary?acc_id=587Small sensory organ with photoreceptor-like sensory cells that is located in the nuchal region of, apparently, all coleoid cephalopods.nuchal organSmall sensory organ with photoreceptor-like sensory cells that is located in the nuchal region of, apparently, all coleoid cephalopods.http://tolweb.org/accessory/Cephalopoda_Glossary?acc_id=587The posterodorsal region of the head and the area immediately posterior to it. nuchal regionThe posterodorsal region of the head and the area immediately posterior to it. http://tolweb.org/accessory/Cephalopoda_Glossary?acc_id=587Prominent transverse ridge in most decapodiforms that extends across the dorsal and along the lateral surfaces of the head at its posterior end.occipital crestProminent transverse ridge in most decapodiforms that extends across the dorsal and along the lateral surfaces of the head at its posterior end.http://tolweb.org/accessory/Cephalopod_Occipital_Region_Terminology?acc_id=1970Fixed folds of the head integument that adjoin the nuchal crest posteriorly and are perpendicular to it. The function of the folds is uncertain.occipital foldFixed folds of the head integument that adjoin the nuchal crest posteriorly and are perpendicular to it. The function of the folds is uncertain.http://tolweb.org/accessory/Cephalopod_Occipital_Region_Terminology?acc_id=1970A membrane connecting the main occipital folds at their posterior ends.occipital membraneA membrane connecting the main occipital folds at their posterior ends.http://tolweb.org/accessory/Cephalopod_Occipital_Region_Terminology?acc_id=1970A chemosensory organ present on the head or neck in all coleoid cephalopods. The olfactory organ is thought to be the homologue of the rhinophore of <strong>Nautilus</strong>.rhinophorecephalopod olfactory organA chemosensory organ present on the head or neck in all coleoid cephalopods. The olfactory organ is thought to be the homologue of the rhinophore of <strong>Nautilus</strong>.http://tolweb.org/accessory/Cephalopoda_Glossary?acc_id=587The progressively descent into a deeper-water habitat as a cephalopod grows older and larger. This distribution pattern is a particularly common in many pelagic cranchiid squids.ontogenetic descentThe progressively descent into a deeper-water habitat as a cephalopod grows older and larger. This distribution pattern is a particularly common in many pelagic cranchiid squids.http://tolweb.org/accessory/Cephalopoda_Glossary?acc_id=587Large lobes of the brain associated with the eyes. In octopods and some squids the optic lobes may be separated from the rest of the brain by an optic stalk of varying length. In <strong>Octopus</strong> the optic lobes contain 92 million cells compared with only 42 million in the main central mass of the brain (J. Young, 1963).optic lobeoptic lobe of brainLarge lobes of the brain associated with the eyes. In octopods and some squids the optic lobes may be separated from the rest of the brain by an optic stalk of varying length. In <strong>Octopus</strong> the optic lobes contain 92 million cells compared with only 42 million in the main central mass of the brain (J. Young, 1963).http://tolweb.org/accessory/Cephalopod_Brain_Terminology?acc_id=1944Capsule in octopodiforms that is embedded in the cephalic cartilage and contains the statocyst capsule.outer statocyst capsuleCapsule in octopodiforms that is embedded in the cephalic cartilage and contains the statocyst capsule.http://tolweb.org/accessory/Cephalopoda_Glossary?acc_id=587Gland surrounding the end of the primary oviduct and responsible for secreting some of the external coatings over spawned eggs or, in incirrates, the cement at the base of the chorion stalk . In octopods it also acts as a spermatheca, and is located around the apparent middle of the oviduct. However, the &quot;distal oviduct&quot; is actually an extension of the oviducal gland. oviducal glandGland surrounding the end of the primary oviduct and responsible for secreting some of the external coatings over spawned eggs or, in incirrates, the cement at the base of the chorion stalk . In octopods it also acts as a spermatheca, and is located around the apparent middle of the oviduct. However, the &quot;distal oviduct&quot; is actually an extension of the oviducal gland. http://tolweb.org/accessory/Cephalopoda_Glossary?acc_id=587First free-living, cephalopod life-history stage that is found in the near-surface plankton and that differs in both morphology and vertical distribution from older juveniles.paralarval stageFirst free-living, cephalopod life-history stage that is found in the near-surface plankton and that differs in both morphology and vertical distribution from older juveniles.http://tolweb.org/accessory/Cephalopoda_Glossary?acc_id=587The long, muscular end of the male gonoduct that assists in transfering spermatophores to the female. Apparently, in species with a hectocotylus, the penis transfers spermatophores to the hectocotylus which in turn transfers them to the female. In species without a hectocotylus, the penis is often greatly elongate, capable of extending beyond the mantle cavity and can, apparently, transfer spermatophores directly to the female.terminal organcephalopod penisWikipediaThe long, muscular end of the male gonoduct that assists in transfering spermatophores to the female. Apparently, in species with a hectocotylus, the penis transfers spermatophores to the hectocotylus which in turn transfers them to the female. In species without a hectocotylus, the penis is often greatly elongate, capable of extending beyond the mantle cavity and can, apparently, transfer spermatophores directly to the female.http://tolweb.org/accessory/Cephalopoda_Glossary?acc_id=587terminal organhttp://tolweb.org/accessory/Cephalopoda_Glossary?acc_id=587Cells in photophores that produce bioluminsecence.photocyteCells in photophores that produce bioluminsecence.http://tolweb.org/accessory/Cephalopod_Photophore_Terminology?acc_id=2015Organ that produces bioluminescence or &quot;living light.&quot; Photophores are often complex with various color filters, reflectors, light guides, lenses and chromatophores surrounding the site of light production, the photogenic region. The name of specific photophores often reflects their position on the animal. For example, the branchial photophore is at the base of the gill, the anal photophore lies at the side of the anus.light organphotophoreOrgan that produces bioluminescence or &quot;living light.&quot; Photophores are often complex with various color filters, reflectors, light guides, lenses and chromatophores surrounding the site of light production, the photogenic region. The name of specific photophores often reflects their position on the animal. For example, the branchial photophore is at the base of the gill, the anal photophore lies at the side of the anus.http://tolweb.org/accessory/Cephalopod_Photophore_Terminology?acc_id=2015Photophores are found in nearly any location in some squid. However, certain locations are the most common. photophore locationPhotophores are found in nearly any location in some squid. However, certain locations are the most common. http://tolweb.org/accessory/Cephalopod_Photophore_Locations?acc_id=1981Non-image forming light-receptive organs located inside the cephalic cartilage in squid and on the stellate ganglion in octopods. They perform a variety of function.photosensitive vesicleNon-image forming light-receptive organs located inside the cephalic cartilage in squid and on the stellate ganglion in octopods. They perform a variety of function.http://tolweb.org/accessory/Cephalopoda_Glossary?acc_id=587A fused pair of lobes that are the anterior-most lobes of the supraesophageal mass of the brain of decapodiforms but is incorporated into the anterior portion of the supraesophageal mass behind the superior buccal lobes in most octopodiforms. inferior frontal lobeposterior buccal lobeA fused pair of lobes that are the anterior-most lobes of the supraesophageal mass of the brain of decapodiforms but is incorporated into the anterior portion of the supraesophageal mass behind the superior buccal lobes in most octopodiforms. http://tolweb.org/accessory/Cephalopoda_Glossary?acc_id=587inferior frontal lobeLarge glands surrounding the buccal mass just posterior to the lips. They are especially well-developed in stauroteuthid cirrates.posterior lip glandLarge glands surrounding the buccal mass just posterior to the lips. They are especially well-developed in stauroteuthid cirrates.http://tolweb.org/accessory/Cephalopoda_Glossary?acc_id=587Glands generally located just posterior to the head whose secretion travels via a duct into the buccal mass.posterior salivary glandGlands generally located just posterior to the head whose secretion travels via a duct into the buccal mass.http://tolweb.org/accessory/Cephalopoda_Glossary?acc_id=587primary conusA thin fold of integument along lateral angles of oral surface of arms and clubs lateral to suckers usually supported by trabeculaeprotective membraneA thin fold of integument along lateral angles of oral surface of arms and clubs lateral to suckers usually supported by trabeculaehttp://www.sil.si.edu/smithsoniancontributions/zoology/pdf_hi/sctz-0513.pdfSome male opisthoteuthid cirrates have enlarged suckers located proximally on the arms (proximal fields) and/or distally on the arms (distal fields).proximal and distal fieldsSome male opisthoteuthid cirrates have enlarged suckers located proximally on the arms (proximal fields) and/or distally on the arms (distal fields).http://tolweb.org/accessory/Cephalopoda_Glossary?acc_id=587A mass of ink and mucous that roughly has the dimensions of the cephalopod that secreted it. pseudomorphA mass of ink and mucous that roughly has the dimensions of the cephalopod that secreted it. http://tolweb.org/accessory/Cephalopod_Pseudomorph_Function?acc_id=1964Refers to an organism that is living or has lived within the past 10,000 years or to object formed or events within the past 10,000 years.obsolete recenttrueRefers to an organism that is living or has lived within the past 10,000 years or to object formed or events within the past 10,000 years.http://tolweb.org/accessory/Geological_Timescale?acc_id=1987Structures in a photophore that reflects bioluminscence.photophore reflectorStructures in a photophore that reflects bioluminscence.http://tolweb.org/accessory/Cephalopod_Photophore_Terminology?acc_id=2015A toothed ribbon that lies in the buccal mass and that aids in movement of food into the esophagus.cephalopod radulaA toothed ribbon that lies in the buccal mass and that aids in movement of food into the esophagus.http://tolweb.org/accessory/Cephalopod_Radula?acc_id=2035Structures that form the nephridium (=kidney). The renal appendages are outpocketings of the veins within the renal sac (primarily the venae cavae) that are covered with renal epithelium. The The renal sac communicates with the mantle cavity via the nephridial pore.kidneynephridiumrenal appendageStructures that form the nephridium (=kidney). The renal appendages are outpocketings of the veins within the renal sac (primarily the venae cavae) that are covered with renal epithelium. The The renal sac communicates with the mantle cavity via the nephridial pore.http://tolweb.org/accessory/Cephalopoda_Glossary?acc_id=587Central axis of the gladius, often thickened, that typically extends the full length of the gladius and sometimes called the median field.rhachismedian fieldrachisCentral axis of the gladius, often thickened, that typically extends the full length of the gladius and sometimes called the median field.http://tolweb.org/accessory/Cephalopod_Gladius_Terminology?acc_id=1955Portion of the gladius that extends posteriorly or posterodorsally from the conus. A distnct rostrum is found only in the Onychoteuthidae, Ancistrocheiridae, Lampadioteuthinae and Vampyroteuthidae. gladiusrostrumPortion of the gladius that extends posteriorly or posterodorsally from the conus. A distnct rostrum is found only in the Onychoteuthidae, Ancistrocheiridae, Lampadioteuthinae and Vampyroteuthidae. http://tolweb.org/accessory/Cephalopoda_Glossary?acc_id=587The region of the shell of cirrates connecting the lateral wings. saddleThe region of the shell of cirrates connecting the lateral wings. http://tolweb.org/accessory/Cephalopoda_Glossary?acc_id=587The shape of the shell with an elongate central region (saddle proper) and broad wings found in cirroteuthid cirrates.saddle-shapedThe shape of the shell with an elongate central region (saddle proper) and broad wings found in cirroteuthid cirrates.http://tolweb.org/accessory/Cephalopoda_Glossary?acc_id=587The most common fin-shape in squids with anterior free fin-lobes, a relatively sharp lateral angle and posterior elongation. See fin shapes. sagittate finThe most common fin-shape in squids with anterior free fin-lobes, a relatively sharp lateral angle and posterior elongation. See fin shapes. http://tolweb.org/accessory/Cephalopoda_Glossary?acc_id=587The skin of the mantle contains scales, tubercules and warts in various species. scales and tuberculeThe skin of the mantle contains scales, tubercules and warts in various species. http://tolweb.org/accessory/Cephalopod_Mantle_Armature?acc_id=1997A conical region at the posterior end of the gladius that is formed by an inrolling and fusion of the vanes. The ventral line of fusion is usually apparent. The secondary conus may be rather short or over half the gladius length.secondary conusA conical region at the posterior end of the gladius that is formed by an inrolling and fusion of the vanes. The ventral line of fusion is usually apparent. The secondary conus may be rather short or over half the gladius length.http://tolweb.org/accessory/Cephalopod_Gladius_Terminology?acc_id=1955An eyelid that covers the ventral part of the cornea. secondary foldsecondary eyelidAn eyelid that covers the ventral part of the cornea. http://tolweb.org/accessory/Cephalopod_Secondary_Eyelid?acc_id=1976A non-muscular fin-shaped structure found in some chiroteuthids, located posterior to the true or primary fin. The secondary fin may act as a buoyancy organ.secondary finA non-muscular fin-shaped structure found in some chiroteuthids, located posterior to the true or primary fin. The secondary fin may act as a buoyancy organ.http://tolweb.org/accessory/Cephalopoda_Glossary?acc_id=587Web that extends from each arm to the primary web in some incirrate octopods. Separation of the arm from the primary web seems to be associated with feeding and/or defense (bell and baloon balloon postures) but the function is not well understood.secondary webWeb that extends from each arm to the primary web in some incirrate octopods. Separation of the arm from the primary web seems to be associated with feeding and/or defense (bell and baloon balloon postures) but the function is not well understood.http://tolweb.org/accessory/Cephalopod_Primary_and_Secondary_Webs?acc_id=1696A reproductive strategy in which females spawn once then die. Sometimes called terminal or &quot;big-bang&quot; spawners. Many cephalopods are semelparous but many are not.semelparousA reproductive strategy in which females spawn once then die. Sometimes called terminal or &quot;big-bang&quot; spawners. Many cephalopods are semelparous but many are not.http://tolweb.org/accessory/Cephalopoda_Glossary?acc_id=587(arm suckers) - A semicrescent plate on the proximal margin of the inner sucker arm rings of the loliginid squid <strong>Uroteuthis</strong>.semicrescent plate(arm suckers) - A semicrescent plate on the proximal margin of the inner sucker arm rings of the loliginid squid <strong>Uroteuthis</strong>.http://tolweb.org/accessory/Cephalopoda_Glossary?acc_id=587Gills of some cirrate octopods that look superficially like gills of sepioids.sepioid gillGills of some cirrate octopods that look superficially like gills of sepioids.http://tolweb.org/accessory/Cephalopoda_Glossary?acc_id=587The sac that secretes the shell in the Coleoidea. The sac is composed of ectodermal epithelium that invaginates during embryonic development to form an internal sac.shell sacThe sac that secretes the shell in the Coleoidea. The sac is composed of ectodermal epithelium that invaginates during embryonic development to form an internal sac.http://tolweb.org/accessory/Cephalopoda_Glossary?acc_id=587Pockets formed by small membranous folds of integument lateral to the foveola in the funnel groove in ommastrephid and thysanoteuthid squids.side pocketPockets formed by small membranous folds of integument lateral to the foveola in the funnel groove in ommastrephid and thysanoteuthid squids.http://tolweb.org/accessory/Cephalopoda_Glossary?acc_id=587The tube-like extension of the body wall, coelom and an external covering tube that penetrates the phragmocone and regulates gas exchange into the phragmocone chambers.siphuncleThe tube-like extension of the body wall, coelom and an external covering tube that penetrates the phragmocone and regulates gas exchange into the phragmocone chambers.http://tolweb.org/accessory/Cephalopoda_Glossary?acc_id=587The coiled rope of sperm that lies within the spermatophore or spermatangia.rope of spermsperm massThe coiled rope of sperm that lies within the spermatophore or spermatangia.http://tolweb.org/accessory/Cephalopod_Spermatophore_Terminology?acc_id=1972Discharged spermatophore which consists of the sperm mass surrounded by a membrane (the inner tunic) with the cement gland at one end.spermatangiaDischarged spermatophore which consists of the sperm mass surrounded by a membrane (the inner tunic) with the cement gland at one end.http://tolweb.org/accessory/Cephalopod_Spermatophore_Terminology?acc_id=1972Specialized sperm-storage structures found in the skin of some female decapodiforms or as pockets of the oviducal gland in octopods.cephalopod spermathecumSpecialized sperm-storage structures found in the skin of some female decapodiforms or as pockets of the oviducal gland in octopods.http://tolweb.org/accessory/Cephalopoda_Glossary?acc_id=587A packet of sperm that is formed by the male and passed to the female during mating. In most coleoids, this packet is very complex and contains a &quot;rope&quot; of sperm (= sperm mass), an ejaculatory apparatus and a cement body. Except for the sperm, the entire structure is non-cellular and consists of a complex architecture of secreted material.spermatophoreA packet of sperm that is formed by the male and passed to the female during mating. In most coleoids, this packet is very complex and contains a &quot;rope&quot; of sperm (= sperm mass), an ejaculatory apparatus and a cement body. Except for the sperm, the entire structure is non-cellular and consists of a complex architecture of secreted material.http://tolweb.org/accessory/Cephalopod_Spermatophore_Terminology?acc_id=1972